Receptor
PDB id Resolution Class Description Source Keywords
6NTU 1.8 Å EC: 2.4.2.30 CRYSTAL STRUCTURE OF HUMAN PARP-1 ART DOMAIN BOUND TO INHIBI 15 HOMO SAPIENS PARP-1 POLY(ADP-RIBOSE) POLYMERASE PARP INHIBITOR PARP1 TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURAL BASIS FOR ALLOSTERIC PARP-1 RETENTION ON BREAKS. SCIENCE V. 368 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1PE A:1104;
 Invalid;
 none;
 submit data
238.278 C10 H22 O6 C(COC...
DMS A:1102;
A:1103;
 Invalid;
Invalid;
 none;
none;
 submit data
78.133 C2 H6 O S CS(=O...
GLC FRU B:1;
 Valid;
 none;
 submit data
340.281 n/a O=CC1...
SO4 A:1106;
A:1107;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
L1S A:1105;
 Valid;
 none;
 submit data
485.495 C25 H23 N7 O4 COC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6NRF 2 Å EC: 2.4.2.30 CRYSTAL STRUCTURE OF HUMAN PARP-1 ART DOMAIN BOUND TO INHIBI HOMO SAPIENS PARP-1 POLY(ADP-RIBOSE) POLYMERASE PARP INHIBITOR PARP1 TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DESIGN AND SYNTHESIS OF POLY(ADP-RIBOSE) POLYMERASE INHIBITORS: IMPACT OF ADENOSINE POCKET-BINDING MOTI APPENDAGE TO THE 3-OXO-2,3-DIHYDROBENZOFURAN-7-CARB ON POTENCY AND SELECTIVITY. J.MED.CHEM. V. 62 5330 2019
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
2 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
3 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
4 6NTU - GLC FRU n/a n/a
5 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
6 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
7 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
2 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
3 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
4 6NTU - GLC FRU n/a n/a
5 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
6 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
7 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5XSU Kd = 180 nM 8E3 C15 H13 F N4 O2 c1c(cc2c(c....
2 4R6E ic50 = 132 nM 3JD C19 H20 N4 O c1cc2cn(nc....
3 4ZZZ Kd = 0.087 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
4 5XSR Kd = 0.000000064 M 8EC C15 H13 F N4 O S c1c(cc2c(c....
5 6VKK - RPB C19 H18 F N3 O CNCc1ccc(c....
6 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
7 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
8 4HHY ic50 = 1.92 nM 15R C33 H30 F N5 O4 c1ccc2c(c1....
9 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
10 5XST ic50 = 27 nM 8E6 C15 H13 F N4 O S c1c(cc2c(c....
11 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
12 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
13 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
14 6XVW - O3H C19 H21 N5 O S c1ccc2c(c1....
15 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
16 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
17 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
18 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
19 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
20 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
21 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
22 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
23 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
24 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
25 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
26 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
27 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
28 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
29 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
30 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
31 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
32 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
33 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
34 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
35 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
36 6NTU - GLC FRU n/a n/a
37 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
38 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
39 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
40 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
41 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
42 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
43 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
44 6I8T - H7Z C21 H29 N3 O2 C[C@@H]1c2....
45 6I8M - H7W C21 H29 N3 O2 C[C@H]1c2c....
46 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GLC FRU; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 GLC FRU 1 1
2 GLC FRU GLA 0.761905 0.972973
3 FRU GLC GLA 0.5 0.921053
4 GLC FRU GLA GLA GLA 0.492958 0.921053
5 GLC FRU GLA GLA 0.492958 0.921053
6 GLC FRU FRU FRU 0.492958 0.921053
7 ZEE UEA FRU FRU FRU 0.492958 0.921053
8 GLC FRU FRU 0.457143 0.921053
9 ARA TT7 4GL 0.445783 0.744681
Ligand no: 2; Ligand: L1S; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 L1S 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: GLC FRU; Similar ligands found: 23
No: Ligand Similarity coefficient
1 GLC Z9N 0.9697
2 MAN MAN 0.9233
3 FRU FRU 0.9109
4 MMA MAN 0.9053
5 RRY RRJ 0.9023
6 BDF GLC 0.9009
7 FRU GLC 0.8988
8 TW7 GLC 0.8931
9 GLC GLC 0.8902
10 GLA GLC 0.8842
11 ADA AQA 0.8838
12 GLC IFM 0.8831
13 4UO 0.8776
14 GLC 7LQ 0.8767
15 GAL GLA 0.8744
16 ADA ADA 0.8733
17 GLC DMJ 0.8705
18 B1T 0.8679
19 9E3 0.8670
20 GLA GLA 0.8647
21 RR7 GLC 0.8636
22 4P8 0.8619
23 CQW 0.8506
Ligand no: 2; Ligand: L1S; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6NRF; Ligand: KYV; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6nrf.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 6W65 T9D 10.3321
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