-->
Receptor
PDB id Resolution Class Description Source Keywords
2RC8 1.45 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE NR3A LIGAND BINDING CORE COMPLEX WI SERINE AT 1.45 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
CL A:295;
A:296;
B:295;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
DSN A:901;
A:902;
Valid;
Valid;
none;
none;
submit data
105.093 C3 H7 N O3 C([C@...
GOL A:903;
A:904;
B:296;
Invalid;
Invalid;
Invalid;
none;
none;
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
2RC8 1.45 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE NR3A LIGAND BINDING CORE COMPLEX WI SERINE AT 1.45 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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 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
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 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 174 families.
1 3OEM - OEM C5 H9 N O4 CN[C@H](CC....
2 3OEN - GLU C5 H9 N O4 C(CC(=O)O)....
3 3OEK - ASP C4 H7 N O4 C([C@@H](C....
4 4JWY - 1N4 C8 H13 N3 O3 CCCc1cnn(c....
5 3OEL - DGL C5 H9 N O4 C(CC(=O)O)....
6 4JWX - 1N4 C8 H13 N3 O3 CCCc1cnn(c....
7 2A5S - GLU C5 H9 N O4 C(CC(=O)O)....
8 2RC9 - 1AC C4 H7 N O2 C1CC1(C(=O....
9 2RC8 - DSN C3 H7 N O3 C([C@H](C(....
10 2RC7 - GLY C2 H5 N O2 C(C(=O)O)N
11 2RCB - DSN C3 H7 N O3 C([C@H](C(....
12 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
13 1Y20 Ki = 4.8 uM 1AC C4 H7 N O2 C1CC1(C(=O....
14 1PB7 - GLY C2 H5 N O2 C(C(=O)O)N
15 1Y1Z Ki = 0.831 mM 192 C5 H9 N O2 C1CC(C1)(C....
16 1PB8 Ki = 7.02 uM DSN C3 H7 N O3 C([C@H](C(....
17 1Y1M Ki = 15.3 mM AC5 C6 H11 N O2 C1CCC(C1)(....
18 1PBQ Ki = 0.54 uM DK1 C10 H5 Cl2 N O3 c1c(cc(c2c....
19 1PB9 Ki = 241 uM 4AX C3 H6 N2 O2 C1[C@H](C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DSN; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 DSN 1 1
2 SER 1 1
3 CYS 0.65 0.84
4 DCY 0.65 0.84
5 ABA 0.6 0.692308
6 2RA 0.6 0.75
7 DBB 0.6 0.692308
8 HSE 0.590909 0.821429
9 C2N 0.571429 0.730769
10 ASP 0.545455 0.714286
11 ASN 0.545455 0.625
12 DAS 0.545455 0.714286
13 DAB 0.521739 0.724138
14 HL5 0.518519 0.814815
15 CSO 0.5 0.636364
16 LEU 0.5 0.642857
17 API 0.5 0.633333
18 HCS 0.5 0.777778
19 NVA 0.5 0.62069
20 AS2 0.5 0.703704
21 CSS 0.48 0.689655
22 DGY 0.47619 0.607143
23 GGL 0.461538 0.655172
24 DGL 0.461538 0.655172
25 GLU 0.461538 0.655172
26 ORN 0.444444 0.689655
27 SLZ 0.433333 0.625
28 11C 0.413793 0.633333
29 UN1 0.413793 0.633333
30 DLY 0.413793 0.666667
31 CME 0.40625 0.666667
32 LYS 0.4 0.645161
33 DHH 0.4 0.612903
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RC8; Ligand: DSN; Similar sites found with APoc: 115
This union binding pocket(no: 1) in the query (biounit: 2rc8.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3NY4 SMX 1.50943
2 4NTC FAD 1.70068
3 1H82 FAD 1.70068
4 1E19 ADP 1.70068
5 4YNM SAM 1.76991
6 5AA4 6X4 2.04082
7 2ZJ3 G6P 2.04082
8 1QFY FAD 2.04082
9 1QFY NAP 2.04082
10 2J4K U5P 2.21239
11 4N9I PCG 2.38095
12 1KOR ARG 2.38095
13 4K91 SIN 2.38095
14 4LZJ 22H 2.38095
15 2YI0 YI0 2.62009
16 2POC BG6 2.72109
17 5H68 AGS 2.72109
18 6B2M COA 2.7972
19 5NE2 DGL 2.8777
20 4ZRB COA 2.91971
21 3DRG ARG PRO PRO GLY PHE SER PRO PHE ALA 3.06122
22 3F3E LEU 3.06122
23 4EPM AMP 3.06122
24 3QF7 ANP 3.06122
25 1F5V FMN 3.33333
26 2GZM DGL 3.37079
27 3Q9T FAY 3.40136
28 5VW2 NAP 3.40136
29 5VW2 FDA 3.40136
30 4TMZ GSP 3.40136
31 5V7I 8Z1 3.40136
32 3EFS BTN 3.43348
33 6BSW UDP 3.7415
34 4AMV F6R 3.7415
35 3HVJ 705 4.0724
36 1ME8 RVP 4.08163
37 5JFL NAD 4.08163
38 1GQ2 NAP 4.08163
39 1WK9 TSB 4.10959
40 3OJF IMJ 4.28016
41 3OJF NDP 4.28016
42 4XVX P33 FDA 4.42177
43 4LEB THR THR THR THR THR THR THR 4.42177
44 4XTX 590 4.44444
45 3T2C 13P 4.7619
46 4ZFL 4NK 4.7619
47 2Q89 6CS 5.05837
48 1P3D UMA 5.10204
49 1JQ3 AAT 5.10204
50 4J56 FAD 5.26316
51 1QSM ACO 5.26316
52 4ZTE 4RL 5.44218
53 1KY8 NAP 5.44218
54 5NI5 8YB 5.44218
55 3WBZ ATP 5.53506
56 1USF FMN 5.61798
57 2YLN CYS 5.65371
58 5OKU 0L1 5.78231
59 5APG EEM 6.48649
60 2WK9 PLG 6.80272
61 2WK9 PLP 6.80272
62 1KYV RBF 6.91824
63 3KV8 FAH 7.19424
64 2YJP CYS 7.2165
65 2IVF MD1 7.48299
66 1N62 MCN 7.63889
67 3UWV 2PG 8.04598
68 2C1X UDP 8.16327
69 2UUU FAD 8.84354
70 2UUU PL3 8.84354
71 3TD3 GLY 8.94309
72 5D6J ATP 9.45946
73 5MW8 ATP 9.52381
74 4DZ1 DAL 9.65251
75 3RK1 ATP 9.70464
76 5JE0 AZ8 9.7166
77 5JE0 SAH 9.7166
78 5MGZ SAH 9.74576
79 2QB8 ATP 10.2041
80 1MOQ GLP 10.5442
81 1H0H 2MD 11.6822
82 5UY8 AMZ 11.9048
83 1QG6 NAD 12.6437
84 1QG6 TCL 12.6437
85 4WQM FAD 13.2653
86 1XT8 CYS 14.0411
87 4ZOH MCN 14.2857
88 2FR6 CTN 14.3836
89 5X0J SEP 14.876
90 5X0J AMP 14.876
91 4C0R GDS 14.9194
92 4YDU ADP 15.3061
93 3AB4 THR 16.8539
94 3HUN ZZ7 19.0476
95 1G51 AMO 20.068
96 4POW OP1 22.2642
97 2VHA GLU 25.4355
98 1HSL HIS 28.9916
99 1II5 GLU 29.1845
100 6H1U ASP 32.4042
101 3VV5 SLZ 32.6923
102 2Y7I ARG 33.1878
103 6GPC ARG 33.3333
104 5ORG 6DB 34.2205
105 3N26 ARG 36.9919
106 1LAF ARG 37.395
107 3ZIA ATP 38.0952
108 4YKI GLY 40.2344
109 5L9O GOP 40.2985
110 4YMX ARG 40.3846
111 4KQP GLN 42.6724
112 4ZV1 ARG 44.206
113 1WDN GLN 45.1327
114 5EHS 2JJ 45.1493
115 5EHS 5OY 45.1493
Pocket No.: 2; Query (leader) PDB : 2RC8; Ligand: DSN; Similar sites found with APoc: 17
This union binding pocket(no: 2) in the query (biounit: 2rc8.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5B0I BOG 2.38095
2 1ZUW DGL 2.57353
3 6BSW CE6 3.7415
4 1N1D C2G 3.87597
5 3H78 BE2 4.08163
6 1P31 EPU 5.10204
7 1H2B NAJ 5.44218
8 2VVL FAD 5.78231
9 4PXL NAD 5.78231
10 1BKC INN 7.03125
11 5KVA SAM 8.99281
12 1U8V FAD 11.5646
13 6C8T EQJ 11.9048
14 5CG1 NAD BBN 12.2449
15 4UP4 GAL NAG 12.585
16 2XCM ADP 17.3913
17 4M38 SAH 23.8095
APoc FAQ
Feedback