GPCRmd

GPCRmd Workbench

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Indicate what you want to display in your molecular representation using the selection options of the GPCRmd Viewer.

You can choose one of the selections we propose or define a new one (Customized selection option) using the NGL selection language.

Protein residues can be indicated as generic GPCR residue numbers (Ballesteros-Weinstein or GPCRdb structure-based numbering).

Visualization and trajectory sharing powered by NGL Viewer and MDsrv.

The hydrogen bonding network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

Mutant and variant information obtained from GPCRdb and gnomAD.

Mouse controls:

Left button hold and move: rotate camera around center.

Left button click: pick atom or distance.

Middle button hold and move: zoom camera in and out.

Middle button click: center camera on atom.

Right button hold and move: translate camera in screen plane.

For more information, see the docs.

GPCRmd Viewer

Adenosine receptor A2a in complex with NECA (2YDV.A)

Simulation report and files

Selection

Structure selection

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Input your selection using the NGL selection language. Generic GPCR residue numbering can also be used (more info here).

Sequence selection

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GPCR conserved positions

Highly conserved residues and motifs

Most conserved residues

Representation:

GPCRmd Toolkit

Interaction frequencies

Hydrogen bonds

Trajectory:

Frames:

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From to

Selection:

Do not include hydrogen bonds between neighbours

All hydrogen bonds

Only side chain hydrogen bonds

Threshold: %

Ligand receptor contacts

Compute interaction between GPCR and

In trajectory:

Stride:

Threshold: Å

Consider

Salt bridges

Trajectory:

Frames:

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Threshold: %

Distance

Select distances from the viewer by clicking on the atoms. Afterwards, import your selections by clicking at the import button (). You can also manually introduce the atom indices.

Compute distance between and

In trajectory:

Stride:

RMSD

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Stride:

Reference: frame from trajectory

Selection:

Protein alpha carbons

Protein CA, CB, C, N, O

Non-hydrogen protein atoms

All protein atoms

N-ethyl-5'-carboxamido adenosine

Breathing motions

We classify GPCR breathing motions in a simulation "open", "intermediate" or "closed". This classification is based on a specific distance between TM2 and TM6, plotted bellow.

Display in viewer

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Download trajectory clustered by conformations:

Filtering trajectory frames. Please be patient, this might take a few minutes....

Water happiness


Display interface waters		Color by:

Show top positions:	80

Plot:

Genetic variants

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Filter by aminoacid change:

Filter by functional site:

Filter by predicted impact:

Position	GPCRdb num	Variant	Variant ID	AA change	Allele frequency	Allele count	Allele number	Functionally relevant site	SIFT score	PolyPhen-2 score	Unified Impact Prediction	PTM site
4	1x30	M - T	rs201121703	changed	6.370e-05	2	31376		0.03	0.053	Benign
6	1x32	S - F	rs752957802	changed					0.1	0.001	Benign
7	1x33	S - L	rs764528797	changed					0.51	0	Benign
8	1x34	V - M	rs1234663298	similar					0.17	0.18	Benign
8	1x34	V - A	rs781747793	similar					0.23	0.001	Benign
11	1x37	T - S	rs1416005026	similar					0.52	0	Benign
11	1x37	T - M	rs779641559	changed	3.190e-05	1	31366		0.23	0.003	Benign
12	1x38	V - M	rs1287369177	similar	3.190e-05	1	31382		0.27	0.254	Benign
13	1x39	E - K	rs1412843557	changed					0	0.991	Damaging
15	1x41	A - T	rs200557920	changed	1.593e-04	5	31378		0.26	0.005	Benign
15	1x41	A - V	rs1277361149	similar					1	0	Benign
16	1x42	I - V	rs1369259880	similar					0.01	0.312	Indef.
19	1x45	L - P	rs1281490879	changed					0.01	0.968	Damaging
21	1x47	I - V	rs200559878	similar					1	0	Benign
22	1x48	L - V	rs1275216931	similar					0.52	0.007	Benign
24	1x50	N - S	rs765343382	similar	3.190e-05	1	31394		0	0.936	Damaging
28	1x54	C - R	rs1432789548	changed	3.190e-05	1	31396		0	0.994	Damaging
28	1x54	C - G	rs1432789548	changed					0	0.994	Damaging
28	1x54	C - S	rs763237836	changed					0	0.98	Damaging
33	1x59	L - R	rs764185917	changed				Intracellular binding site	0.03	0.006	Indef.
35	12x48	S - N	rs1441171313	similar				Intracellular binding site	0.03	0.055	Indef.
38	12x51	Q - E	rs1304649426	changed				Intracellular binding site	0	0.802	Indef.
38	12x51	Q - L	rs1370633042	changed				Intracellular binding site	0	0.946	Damaging
40	2x38	V - I	rs201808263	similar	6.370e-05	2	31388	Intracellular binding site	0.52	0.02	Benign
45	2x43	V - L	rs1340634508	similar				Intracellular binding site	0.54	0.025	Benign
48	2x46	L - P	rs1270949962	changed					0	1	Damaging
49	2x47	A - V	rs748680136	similar					0	0.999	Damaging
50	2x48	A - V	rs4530	similar	7.616e-03	239	31382		1	0.011	Benign
52	2x50	D - N	rs199999926	changed	3.190e-05	1	31388	CM: Na binding site	0	1	Damaging
54	2x52	A - T	rs770703350	changed					0.01	0.931	Damaging
56	2x54	G - D	rs1461647498	changed					0	1	Damaging
58	2x551	L - V	rs1439210381	similar					0.02	0.345	Indef.
59	2x56	A - T	rs775666461	changed				Binding site	0.02	0.955	Damaging
60	2x57	I - V	rs764430333	similar					0.06	0.82	Benign
60	2x57	I - T	rs1336987825	changed					0	1	Damaging
66	2x63	I - V	rs774685876	similar				Binding site	0.05	0.355	Indef.
68	2x65	T - S	rs1467287315	similar					0.09	0.05	Benign
68	2x65	T - I	rs750761186	changed					0.67	0.005	Benign
69	2x66	G - R	rs766756975	changed					0	1	Damaging
72	23x52	A - T	rs139287520	changed					1	0.074	Benign
72	23x52	A - V	rs778601588	similar					0.25	0.057	Benign
73	3x21	A - T	rs1163539529	changed					0.54	0.001	Benign
82	3x30	C - Y	rs200860724	changed					0	0.997	Damaging
84	3x32	V - I	rs201860587	similar				Binding site	0.03	0.079	Indef.
88	3x36	T - R	rs746738083	changed				Binding site	0	1	Damaging
89	3x37	Q - H	rs780974436	changed				Binding site	0	1	Damaging
99	3x47	A - T	rs1261102428	changed					0.03	0.611	Indef.
102	3x50	R - G	rs1203342580	changed	3.180e-05	1	31404	CM: ionic lock	0	1	Damaging
102	3x50	R - C	rs1203342580	changed				CM: ionic lock	0	1	Damaging
102	3x50	R - H	rs768616769	similar	3.180e-05	1	31398	CM: ionic lock	0.03	1	Damaging
104	3x52	I - M	rs1485953994	similar					0	0.545	Indef.
105	3x53	A - T	rs774773657	changed				Intracellular binding site	0.08	0.997	Indef.
107	3x55	R - S	rs200937140	changed				Intracellular binding site	0.02	0.02	Indef.
107	3x55	R - C	rs200937140	changed				Intracellular binding site	0.02	0.02	Indef.
110	34x51	L - I	rs998459173	similar				Intracellular binding site	0.07	0.986	Indef.
111	34x52	R - W	rs773743606	changed				Intracellular binding site	0	0.82	Indef.
115	34x56	L - F	rs779140681	changed				Intracellular binding site	0	0.76	Indef.
116	34x57	V - M	rs748198311	similar				Intracellular binding site	0.05	0.789	Indef.
118	4x39	G - C	rs200688325	changed	3.190e-05	1	31386	Intracellular binding site	0.01	0.524	Indef.
118	4x39	G - D	rs866947347	changed				Intracellular binding site	0.04	0.939	Damaging
119	4x40	T - M	rs942698715	changed	3.190e-05	1	31376	Intracellular binding site	0.12	0.068	Benign
123	4x44	G - D	rs776995788	changed					0.2	0.721	Benign
125	4x46	I - T	rs200176420	changed					0	0.927	Damaging
130	4x51	V - M	rs765688222	similar					0.03	0.882	Indef.
133	4x54	F - I	rs1479461678	changed					0.24	0.087	Benign
136	4x57	G - S	rs757137296	changed	3.190e-05	1	31378	Binding site	0	1	Damaging
140	4x61	M - V	rs1430794713	similar					0	0.043	Indef.
140	4x61	M - I	rs767230391	similar					0.01	0.24	Indef.
141	4x62	L - Q	rs201332411	changed					0	0.979	Damaging
144		N - K	rs8192446	changed					0	0.761	Indef.
147		G - S	rs78720419	changed	1.351e-02	424	31386		0.04	0.527	Indef.
147		G - C	rs78720419	changed	3.190e-05	1	31386		0.04	0.527	Indef.
148		Q - K	rs1439944763	changed					0.53	0	Benign
148		Q - R	rs778113831	changed					0.49	0	Benign
154		N - S	rs1294240504	similar					0.03	0.296	Indef.	Glycosylation
154		N - K	rs1467567343	changed	3.190e-05	1	31394		0.1	0.021	Benign	Glycosylation
156		S - T	rs758431179	similar					0.03	0.41	Indef.
156		S - Y	rs1234776604	changed					0.01	0.676	Indef.
160		G - R	rs150249680	changed	2.230e-04	7	31386		0.52	0.005	Benign
161		E - K	rs763584556	changed					0.57	0.066	Benign
161		E - V	rs1187570205	changed					0.16	0.044	Benign
162		G - S	rs1418918570	changed	3.190e-05	1	31392		0.66	0.132	Benign
165		A - S	rs77393092	changed					0.61	0.011	Benign
166	45x50	C - S	rs1418930522	changed				Binding site	0	0.999	Damaging	Disulfide Bond
171		V - M	rs1461108349	similar					0.01	0.979	Damaging
173	5x36	P - H	rs1431434378	changed				Binding site	0.02	0.958	Damaging
174	5x37	M - V	rs755952858	similar				Binding site	0	0.922	Damaging
177	5x40	M - V	rs1288170983	similar				Binding site	0	0.992	Damaging
179	5x411	Y - H	rs141732109	changed					0	0.991	Damaging
180	5x42	F - S	rs753812201	changed					0	0.93	Damaging
183	5x45	F - S	rs147072171	changed					0	0.993	Damaging
184	5x46	A - T	rs200446971	changed	9.560e-05	3	31386		0.11	0.927	Indef.
186	5x47	V - M	rs747066875	similar				Binding site	0	0.961	Damaging
191	5x52	L - P	rs1263151194	changed					0	0.989	Damaging
192	5x53	L - P	rs757441319	changed					0	0.977	Damaging
195	5x56	G - C	rs1258245188	changed					0.04	0.782	Indef.
195	5x56	G - A	rs201680338	changed					0.28	0.001	Benign
198	5x59	L - V	rs1409917906	similar					0.44	0.001	Benign
199	5x60	R - W	rs199767901	changed					0.02	0.082	Indef.
199	5x60	R - Q	rs746275437	changed	3.190e-05	1	31386		0.04	0.047	Indef.
201	5x62	F - L	rs1436493786	changed					0.02	0.921	Damaging
203	5x64	A - V	rs780599770	similar				Intracellular binding site	1	0.125	Benign
205	5x66	R - Q	rs773766284	changed				Intracellular binding site	0.04	0.968	Damaging
206	5x67	R - Q	rs771672458	changed	3.190e-05	1	31374	Intracellular binding site	0.08	0.116	Benign
212	5x73	E - K	rs201891365	changed				Intracellular binding site	0.15	0.013	Benign
215		P - L	rs753620615	changed	3.190e-05	1	31394		0.38	0	Benign
217		P - S	rs1234856664	changed					0.61	0.034	Benign
217		P - R	rs199725333	changed					0.16	0.726	Benign
217		P - L	rs199725333	changed	3.190e-05	1	31372		0.16	0.726	Benign
220	6x22	R - W	rs939477540	changed					0	0.96	Damaging
220	6x22	R - Q	rs757325519	changed					0.09	0.049	Benign
222	6x24	R - G	rs781339364	changed				Intracellular binding site	0	0.994	Damaging
222	6x24	R - W	rs781339364	changed	9.560e-05	3	31372	Intracellular binding site	0	0.994	Damaging
222	6x24	R - Q	rs201346032	changed	1.275e-04	4	31376	Intracellular binding site	0.14	0.301	Benign
226	6x28	Q - P	rs1440946966	changed				Intracellular binding site	0.01	0.977	Damaging
228	6x30	E - D	rs138352666	similar				CM: ionic lock	0.02	0.997	Damaging
229	6x31	V - I	rs747653711	similar					0.41	0.042	Benign
241	6x43	L - F	rs1198871098	changed					0.05	0.43	Indef.
242	6x44	F - S	rs760407585	changed				Binding site	0	0.999	Damaging
243	6x45	A - V	rs371233023	similar	3.190e-05	1	31378		0.02	0.884	Indef.
251	6x53	I - N	rs1198199300	changed					0	0.95	Damaging
254	6x56	C - R	rs1236154233	changed				Binding site	0	0.998	Damaging
259	6x61	C - Y	rs1469687995	changed	3.190e-05	1	31376		0.06	0.569	Benign	Disulfide Bond
259	6x61	C - F	rs1469687995	changed					0.06	0.569	Benign	Disulfide Bond
261		D - N	rs146268015	changed	6.370e-05	2	31380		0.58	0	Benign
262		C - G	rs761858787	changed					0.02	0.281	Indef.	Disulfide Bond
264		H - Y	rs1169156621	changed					0.11	0.042	Benign
265		A - T	rs767602595	changed					0.44	0.127	Benign
270	7x34	M - T	rs756360364	changed				Binding site	0.05	0.677	Benign
273	7x37	A - G	rs780201352	changed				Binding site	0.16	0.743	Benign
275	7x39	V - I	rs141942830	similar	2.548e-04	8	31396	Binding site	1	0	Benign
280	7x45	N - S	rs779344683	similar				CM: Na binding site	0	0.779	Indef.
281	7x46	S - L	rs748699595	changed				CM: Na binding site	0	0.999	Damaging
283	7x48	V - A	rs1489285016	similar	3.190e-05	1	31394		0	0.991	Damaging
289	7x54	A - P	rs201077707	changed					0	0.995	Damaging
289	7x54	A - T	rs201077707	changed					0	0.995	Damaging
289	7x54	A - V	rs1266338168	similar					0	0.706	Indef.
290	7x55	Y - N	rs1268412903	changed	3.190e-05	1	31396	Intracellular binding site	0.01	0.965	Damaging
290	7x55	Y - F	rs202222894	similar	3.180e-05	1	31398	Intracellular binding site	0.42	0.044	Benign
291	7x56	R - C	rs745714462	changed				Intracellular binding site	0	0.791	Indef.
291	7x56	R - H	rs769621641	similar				Intracellular binding site	0.03	0.352	Indef.
293	8x48	R - C	rs142560733	changed	3.180e-05	1	31404	Intracellular binding site	0	0.969	Damaging
293	8x48	R - H	rs201025926	similar	3.180e-05	1	31398	Intracellular binding site	0.01	0.934	Damaging
294	8x49	E - K	rs1390389374	changed				Intracellular binding site	0.03	0.892	Indef.
294	8x49	E - Q	rs1390389374	changed				Intracellular binding site	0.03	0.892	Indef.
294	8x49	E - D	rs773303136	similar				Intracellular binding site	0.43	0.007	Benign
295	8x50	F - L	rs17650937	changed					0	0.894	Indef.
296	8x51	R - C	rs201181215	changed					0	0.811	Indef.
296	8x51	R - H	rs199792438	similar					0	0.904	Indef.
300	8x55	R - H	rs4990	similar	3.190e-05	1	31394		0.33	0.137	Benign
300	8x55	R - L	rs4990	changed					0.33	0.137	Benign
304	8x59	R - C	rs201666195	changed	3.180e-05	1	31406		0.01	0.038	Indef.
304	8x59	R - H	rs199666600	similar	1.592e-04	5	31400		0.15	0.003	Benign
306	8x61	H - R	rs778398772	similar					0.06	0.019	Benign
306	8x61	H - Q	rs200799056	changed					0.03	0.145	Indef.
307	8x62	V - I	rs200117692	similar	6.370e-05	2	31404		1	0	Benign
308	8x63	L - P	rs781051901	changed					0	0.968	Damaging
309	8x64	R - K	rs149670419	similar					1	0.07	Benign

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