Receptor
PDB id Resolution Class Description Source Keywords
2rca 1.58 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WI AT 1.58 ANGSTROM RESOLUTION RATTUS NORVEGICUS MEMBRANE PROTEIN CELL JUNCTION GLYCOPROTEIN ION TRANSPORTCHANNEL MAGNESIUM POSTSYNAPTIC CELL MEMBRANE RECEPTOR STRANSMEMBRANE TRANSPORT
Ref.: MOLECULAR MECHANISM OF LIGAND RECOGNITION BY NR3 SU GLUTAMATE RECEPTORS. EMBO J. V. 27 2158 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLY A:901;
A:902;
Valid;
Valid;
none;
none;
Kd = 16.4 nM
75.067 C2 H5 N O2 C(C(=...
GOL A:903;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RCA 1.58 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WI AT 1.58 ANGSTROM RESOLUTION RATTUS NORVEGICUS MEMBRANE PROTEIN CELL JUNCTION GLYCOPROTEIN ION TRANSPORTCHANNEL MAGNESIUM POSTSYNAPTIC CELL MEMBRANE RECEPTOR STRANSMEMBRANE TRANSPORT
Ref.: MOLECULAR MECHANISM OF LIGAND RECOGNITION BY NR3 SU GLUTAMATE RECEPTORS. EMBO J. V. 27 2158 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 224 families.
1 2RCB - DSN C3 H7 N O3 C([C@H](C(....
2 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 172 families.
1 2RC9 - 1AC C4 H7 N O2 C1CC1(C(=O....
2 2RC8 - DSN C3 H7 N O3 C([C@H](C(....
3 2RC7 - GLY C2 H5 N O2 C(C(=O)O)N
4 2RCB - DSN C3 H7 N O3 C([C@H](C(....
5 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 145 families.
1 1PB8 Ki = 7.02 uM DSN C3 H7 N O3 C([C@H](C(....
2 1Y20 Ki = 4.8 uM 1AC C4 H7 N O2 C1CC1(C(=O....
3 1PB7 - GLY C2 H5 N O2 C(C(=O)O)N
4 1Y1Z Ki = 0.831 mM 192 C5 H9 N O2 C1CC(C1)(C....
5 1Y1M Ki = 15.3 mM AC5 C6 H11 N O2 C1CCC(C1)(....
6 1PBQ Ki = 0.54 uM DK1 C10 H5 Cl2 N O3 c1c(cc(c2c....
7 1PB9 Ki = 241 uM 4AX C3 H6 N2 O2 C1[C@H](C(....
8 3OEM - OEM C5 H9 N O4 CN[C@H](CC....
9 3OEN - GLU C5 H9 N O4 C(CC(=O)O)....
10 3OEK - ASP C4 H7 N O4 C([C@@H](C....
11 4JWY - 1N4 C8 H13 N3 O3 CCCc1cnn(c....
12 3OEL - DGL C5 H9 N O4 C(CC(=O)O)....
13 4JWX - 1N4 C8 H13 N3 O3 CCCc1cnn(c....
14 2A5S - GLU C5 H9 N O4 C(CC(=O)O)....
15 2RC9 - 1AC C4 H7 N O2 C1CC1(C(=O....
16 2RC8 - DSN C3 H7 N O3 C([C@H](C(....
17 2RC7 - GLY C2 H5 N O2 C(C(=O)O)N
18 2RCB - DSN C3 H7 N O3 C([C@H](C(....
19 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands
Ligand no: 1; 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
Pocket no: 1; Query (leader) PDB : 2RCA; Ligand: GLY; Similar sites found: 108
This union binding pocket (no: 1) in the query (biounit: 2rca.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 2RCA GLY 4.23e-14 1
2 2RC8 DSN 1.19e-12 0.98984
3 3OEN GLU 4.833e-10 0.79505
4 4IO2 GLU 3.809e-09 0.74592
5 1M5B BN1 1.346e-07 0.73387
6 3QXM NDZ 9.469e-09 0.73241
7 4NF6 GLY 8.484e-09 0.71377
8 2V3U DSN 2.762e-08 0.68407
9 3FAS GLU 2.247e-08 0.6824
10 2PYY GLU 8.512e-08 0.66687
11 3FV1 DYH 4.516e-07 0.65706
12 2VHA GLU 2.578e-07 0.63762
13 4JWX 1N4 1.692e-07 0.63497
14 1XT8 CYS 1.131e-06 0.59908
15 4KQP GLN 1.307e-05 0.55096
16 2YJP CYS 8.614e-06 0.5459
17 4G4P GLN 2.127e-05 0.53828
18 2Q2A ARG 3.322e-05 0.53635
19 4NF6 2JL 0.0001383 0.51254
20 4DZ1 DAL 6.811e-06 0.50831
21 1PBQ DK1 0.000132 0.49881
22 1LAF ARG 0.0001537 0.48755
23 4POW OP1 0.0008137 0.47543
24 2UUU FAD 0.00762 0.47106
25 3DRG ARG 0.004224 0.46433
26 2POC BG6 0.001503 0.4431
27 2WK9 PLG 0.007541 0.4419
28 2WK9 PLP 0.008002 0.44081
29 3VV5 SLZ 0.00236 0.43867
30 3N26 ARG 0.002301 0.43761
31 4C0R GDS 0.006964 0.4278
32 3ZEU AGS 0.008264 0.42763
33 2Y7I ARG 0.003295 0.42598
34 3BWY DNC 0.01668 0.42557
35 1ZQ5 E04 0.04873 0.42421
36 2YLN CYS 0.004618 0.42421
37 4HA6 FAD 0.0245 0.4212
38 3WBZ ATP 0.006183 0.42094
39 3TD3 GLY 0.006706 0.41649
40 1QFY NAP 0.02453 0.41537
41 1NQU RDL 0.01485 0.41462
42 1JQ3 AAT 0.02287 0.41192
43 2IVF MD1 0.02534 0.41147
44 3HVJ 705 0.02905 0.41126
45 1HXD BTN 0.02621 0.4069
46 1QF9 ADP 0.04554 0.40541
47 4G8N G8M 0.04086 0.40463
48 2C1X UDP 0.02817 0.40435
49 2GZM DGL 0.01539 0.40414
50 4F2O QUS 0.03901 0.4016
51 1EJB INJ 0.02025 0.40159
52 4LZJ 22H 0.03139 0.40134
53 4CNG SAH 0.03286 0.40129
54 3ZIA ATP 0.02012 0.40004
55 3NY4 SMX 0.04132 0.39785
56 1WK9 TSB 0.01315 0.39755
57 1PKX XMP 0.02723 0.39699
58 1HYH NAD 0.03537 0.39633
59 2VVT DGL 0.04851 0.3959
60 1W7F ICT 0.01256 0.3955
61 1P31 EPU 0.04194 0.39519
62 4TMZ GSP 0.0448 0.3946
63 2DT5 NAD 0.04446 0.39457
64 1YC4 43P 0.0191 0.39456
65 4MCB 21W 0.03744 0.39454
66 4M38 SAH 0.03979 0.3943
67 3GDH SAH 0.04647 0.39405
68 1OG1 TAD 0.03121 0.39327
69 1O94 AMP 0.02825 0.39326
70 3EFS BTN 0.03954 0.39279
71 4O67 1SY 0.03586 0.39093
72 1O97 AMP 0.04355 0.39079
73 1E19 ADP 0.02898 0.39035
74 3ZOA ACR 0.01275 0.39019
75 2JFN GLU 0.0176 0.38942
76 4FUT ATP 0.0343 0.38695
77 3HBN UDP 0.03537 0.38664
78 2CXS F6P 0.03667 0.38521
79 1KOJ PAN 0.04689 0.38474
80 3ZIA ADP 0.0374 0.38186
81 2D0O ADP 0.04215 0.38157
82 3I59 N6R 0.03908 0.3813
83 1KZN CBN 0.03435 0.38117
84 4MUV PCG 0.03341 0.38033
85 2Q89 6CS 0.01771 0.37953
86 1BKC INN 0.04225 0.37902
87 4BGB ADP 0.03852 0.379
88 3A1S GDP 0.04054 0.37886
89 3I54 CMP 0.04327 0.37814
90 1UNQ 4IP 0.03521 0.37768
91 1C96 FLC 0.03775 0.37629
92 1GT6 OLA 0.04336 0.37244
93 1GPM CIT 0.02385 0.3707
94 4FE2 AIR 0.04708 0.36982
95 4JBL MET 0.04654 0.36965
96 3G2Y GF4 0.01966 0.36847
97 3SHR CMP 0.04967 0.36839
98 3Q72 GNP 0.04964 0.36707
99 1ZUW DGL 0.04101 0.36613
100 2DWU DGL 0.0412 0.366
101 1WZU MLT 0.03828 0.36502
102 1A8U BEZ 0.04955 0.36439
103 2CZL TLA 0.02923 0.36412
104 4I8E RMY 0.0484 0.3632
105 1XFF GLU 0.04939 0.36312
106 1VRP IOM 0.03107 0.35697
107 1SQL GUN 0.03867 0.35267
108 3ITA AIC 0.02688 0.35139
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