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Receptor
PDB id Resolution Class Description Source Keywords
5DEX 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN1/GLUN2A NMDA RECEPTOR AGONIST BIND DOMAINS WITH GLYCINE AND ANTAGONIST, PHENYL-ACEPC RATTUS NORVEGICUS TRANSPORT PROTEIN RECEPTOR
Ref.: STRUCTURAL BASIS OF SUBUNIT SELECTIVITY FOR COMPETI RECEPTOR ANTAGONISTS WITH PREFERENCE FOR GLUN2A OVE SUBUNITS. PROC. NATL. ACAD. SCI. 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5E0 B:301;
Valid;
none;
Ki = 22.6 nM
275.26 C13 H13 N3 O4 c1ccc...
GLY A:1001;
Valid;
none;
submit data
75.067 C2 H5 N O2 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DEX 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN1/GLUN2A NMDA RECEPTOR AGONIST BIND DOMAINS WITH GLYCINE AND ANTAGONIST, PHENYL-ACEPC RATTUS NORVEGICUS TRANSPORT PROTEIN RECEPTOR
Ref.: STRUCTURAL BASIS OF SUBUNIT SELECTIVITY FOR COMPETI RECEPTOR ANTAGONISTS WITH PREFERENCE FOR GLUN2A OVE SUBUNITS. PROC. NATL. ACAD. SCI. 2017 U.S.A.
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 5VII Ki = 51.8 nM 5DY C16 H18 F N3 O4 c1cc(ccc1C....
2 5H8F - GLY C2 H5 N O2 C(C(=O)O)N
3 2A5T - GLY C2 H5 N O2 C(C(=O)O)N
4 5VIJ Ki = 24.3 nM 5DX C13 H12 Br N3 O4 c1cc(ccc1n....
5 5I57 - GLY C2 H5 N O2 C(C(=O)O)N
6 5H8Q - 5YE C18 H18 F N3 O S CCN(CC1=CC....
7 5U8C ic50 = 68.4 nM 84J C17 H17 Br N3 O5 P C[C@@H](c1....
8 5KCJ - GLY C2 H5 N O2 C(C(=O)O)N
9 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
10 5H8N - 5YD C20 H18 F N3 O3 S c1cc(cnc1)....
11 5TPA - GLY C2 H5 N O2 C(C(=O)O)N
12 4NF8 - GLU C5 H9 N O4 C(CC(=O)O)....
13 5KDT - GLU C5 H9 N O4 C(CC(=O)O)....
14 4NF4 - GLU C5 H9 N O4 C(CC(=O)O)....
15 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
16 5TP9 - GLU C5 H9 N O4 C(CC(=O)O)....
17 5VIH Ki = 32.2 nM 5DZ C13 H12 F N3 O4 c1cc(ccc1n....
18 5H8H - GLY C2 H5 N O2 C(C(=O)O)N
19 5I59 ic50 = 641 nM 67Q C18 H19 F2 N5 O3 S2 Cc1c(ncc(n....
20 4NF6 Ki = 0.82 uM 2JL C21 H18 N2 O5 c1ccc2c(c1....
21 5I56 ic50 = 1530 nM 67P C21 H17 Cl F N3 O4 S c1ccc(cc1)....
22 5I2N - GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5VII Ki = 51.8 nM 5DY C16 H18 F N3 O4 c1cc(ccc1C....
2 5H8F - GLY C2 H5 N O2 C(C(=O)O)N
3 2A5T - GLY C2 H5 N O2 C(C(=O)O)N
4 5VIJ Ki = 24.3 nM 5DX C13 H12 Br N3 O4 c1cc(ccc1n....
5 5I57 - GLY C2 H5 N O2 C(C(=O)O)N
6 5H8Q - 5YE C18 H18 F N3 O S CCN(CC1=CC....
7 5U8C ic50 = 68.4 nM 84J C17 H17 Br N3 O5 P C[C@@H](c1....
8 5KCJ - GLY C2 H5 N O2 C(C(=O)O)N
9 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
10 5H8N - 5YD C20 H18 F N3 O3 S c1cc(cnc1)....
11 5TPA - GLY C2 H5 N O2 C(C(=O)O)N
12 4NF8 - GLU C5 H9 N O4 C(CC(=O)O)....
13 5KDT - GLU C5 H9 N O4 C(CC(=O)O)....
14 4NF4 - GLU C5 H9 N O4 C(CC(=O)O)....
15 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
16 5TP9 - GLU C5 H9 N O4 C(CC(=O)O)....
17 5VIH Ki = 32.2 nM 5DZ C13 H12 F N3 O4 c1cc(ccc1n....
18 5H8H - GLY C2 H5 N O2 C(C(=O)O)N
19 5I59 ic50 = 641 nM 67Q C18 H19 F2 N5 O3 S2 Cc1c(ncc(n....
20 4NF6 Ki = 0.82 uM 2JL C21 H18 N2 O5 c1ccc2c(c1....
21 5I56 ic50 = 1530 nM 67P C21 H17 Cl F N3 O4 S c1ccc(cc1)....
22 5I2N - GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 families.
1 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5E0; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 5E0 1 1
2 5DX 0.732143 0.921569
3 5DZ 0.724138 0.921569
4 5DY 0.636364 0.903846
Ligand no: 2; Ligand: GLY; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY 1 1
2 BAL 0.5625 0.708333
3 ABU 0.473684 0.708333
4 MCR 0.466667 0.65
5 2RA 0.421053 0.692308
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DEX; Ligand: GLY; Similar sites found with APoc: 58
This union binding pocket(no: 1) in the query (biounit: 5dex.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3HUN ZZ7 2.05479
2 4WQM FAD 2.73973
3 5L13 6ZE 2.82686
4 2D1S SLU 3.08219
5 5B4B LP5 3.22581
6 1N2X SAM 3.53357
7 2ZJ3 G6P 3.53357
8 3N2S FMN 3.61446
9 4PPF FLC 3.76712
10 4ZTE 4RL 3.79147
11 5NJI 8Z2 4.24028
12 5KBF CMP 4.24028
13 2EVL GAL SPH EIC 4.30622
14 5AA4 6X4 4.59364
15 4TVD BGC 4.59364
16 5UAV NDP 4.59364
17 5UAV TFB 4.59364
18 2ISJ FMN 4.78261
19 1KZN CBN 4.87805
20 2POC BG6 5.13699
21 5WKC FAD 5.30035
22 1BKJ FMN 5.41667
23 5J6C FMN 5.47264
24 4AMV F6R 5.47945
25 3F3E LEU 7.42049
26 5K8S CMP 8.10811
27 1WK9 TSB 8.21918
28 2CJF RP4 8.28025
29 1P4A PCP 9.82456
30 5YAK FMN 9.84848
31 4C0R GDS 10.0806
32 2YLN CYS 10.6007
33 3VV5 SLZ 11.1538
34 2C49 ADN 11.6438
35 2Q89 6CS 12.0623
36 2PHN GDP 12.2047
37 1T36 U 14.1343
38 3N26 ARG 15.8537
39 1XT8 CYS 18.4932
40 2YJP CYS 18.8356
41 4YMX ARG 23.4615
42 2VHA GLU 25.0883
43 6H1U ASP 26.1324
44 4DZ1 DAL 28.9575
45 6GPC ARG 32.5397
46 5L9O GOP 32.8358
47 1LAF ARG 33.1933
48 2Y7I ARG 34.0611
49 1II5 GLU 35.1931
50 5ORG 6DB 38.0228
51 4POW OP1 38.1132
52 4KQP GLN 38.7931
53 1HSL HIS 39.0756
54 1WDN GLN 41.5929
55 5EHS 2JJ 44.7761
56 5EHS 5OY 44.7761
57 4ZV1 ARG 45.4936
58 4YKI GLY 47.6562
Pocket No.: 2; Query (leader) PDB : 5DEX; Ligand: 5E0; Similar sites found with APoc: 82
This union binding pocket(no: 2) in the query (biounit: 5dex.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3JYY PPV 2.12014
2 3FXU TSU 2.82686
3 4W9N TCL 2.82686
4 2DVZ GLU 3.08219
5 1UI0 URA 3.41463
6 2X0K PPV 3.42466
7 3WMX THR 3.53357
8 2ZFZ ARG 3.79747
9 3BY9 SIN 3.84615
10 1PIG BGC 3.88693
11 3TY3 GGG 3.88693
12 3K5I AIR 3.97022
13 3CQO FUC 4.10959
14 4LUS TCE 4.10959
15 2G2Y MLI 4.24028
16 5U0L 8YP 4.24028
17 3URB DPF 4.45205
18 3H9A PPY 4.52675
19 6F3G CJN 4.59364
20 5AA4 6X4 4.59364
21 5TQZ GLC 4.66667
22 3ITJ CIT 4.79452
23 1BVY FMN 4.79452
24 4RHS SIA SIA GAL 4.91803
25 2QES ADE 4.98084
26 3ZVS MLI 5
27 4MBY BGC SIA GAL 5.03597
28 2POC BG6 5.13699
29 2UVO NAG 5.26316
30 4AML GYU 5.26316
31 1SNN 5RP 5.28634
32 1LDN FBP 5.30035
33 4TQK NAG 5.30035
34 3LTW HLZ 5.35714
35 4AMV F6R 5.47945
36 3CL5 SIO 6.00707
37 6B2W AG2 6.00707
38 1RVV INI 6.49351
39 5NXX 3Q7 6.71642
40 3THR C2F 7.06714
41 2WGV CIT 7.25806
42 3HQP OXL 7.42049
43 1TKU 5RP 7.84314
44 3B8I OXL 8.01394
45 1XXR MAN 8.07453
46 2HYR BGC GLC 8.19672
47 2GUD MAN 8.19672
48 2NUO BGC 8.19672
49 2NU5 NAG 8.19672
50 2GUC MAN 8.19672
51 2HYQ MAN MAN 8.19672
52 2GUD BMA 8.19672
53 5MB4 NAG 8.48057
54 1N0U SO1 8.48057
55 2DC1 CIT 8.8983
56 6CGZ HL6 10.2837
57 2BCG GER 10.6164
58 1GPM AMP 10.9589
59 1M0W 3GC 11.3014
60 1PS6 4TP 12.6712
61 3BZ3 YAM 12.6812
62 1ZED PNP 13.7809
63 4RF7 ARG 14.1343
64 1KJ1 MAN 18.3486
65 5GVR LMR 18.3761
66 1XT8 CYS 18.4932
67 2YJP CYS 18.8356
68 4KQ6 DLZ 19.0813
69 2VHA GLU 25.0883
70 6H1U ASP 26.1324
71 4DZ1 DAL 28.9575
72 6GPC ARG 32.5397
73 5L9O GOP 32.8358
74 1II5 GLU 35.1931
75 4POW OP1 38.1132
76 4KQP GLN 38.7931
77 1HSL HIS 39.0756
78 1WDN GLN 41.5929
79 5EHS 5OY 44.7761
80 5EHS 2JJ 44.7761
81 4ZV1 ARG 45.4936
82 4YKI GLY 47.6562
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