Receptor
PDB id Resolution Class Description Source Keywords
4L6S 2.2 Å EC: 2.4.2.30 PARP COMPLEXED WITH BENZO[1,4]OXAZIN-3-ONE INHIBITOR HOMO SAPIENS DNA SINGLE-STRAND BREAK REPAIR SENSITIZE TUMORS DNA REPAIR DRD TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DISCOVERY OF NOVEL BENZO[B][1,4]OXAZIN-3(4H)-ONES A POLY(ADP-RIBOSE)POLYMERASE INHIBITORS BIOORG.MED.CHEM.LETT. V. 23 4501 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1WQ B:1100;
A:1100;
Valid;
Valid;
none;
none;
Kd = 0.003 uM
368.857 C21 H21 Cl N2 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4PJT 2.35 Å EC: 2.4.2.30 STRUCTURE OF PARP1 CATALYTIC DOMAIN BOUND TO INHIBITOR BMN 6 HOMO SAPIENS PARP1 INHIBITOR COMPLEX TRANSFERASE-TRANSFERASE INHIBITOR
Ref.: STRUCTURAL BASIS FOR THE INHIBITION OF POLY(ADP-RIB POLYMERASES 1 AND 2 BY BMN 673, A POTENT INHIBITOR FROM DIHYDROPYRIDOPHTHALAZINONE. ACTA CRYSTALLOGR.,SECT.F V. 70 1143 2014
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4R6E ic50 = 132 nM 3JD C19 H20 N4 O c1cc2cn(nc....
2 4ZZZ Kd = 0.087 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
3 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
4 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
5 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
6 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
7 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
8 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
9 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4R6E ic50 = 132 nM 3JD C19 H20 N4 O c1cc2cn(nc....
2 4ZZZ Kd = 0.087 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
3 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
4 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
5 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
6 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
7 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
8 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
9 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
10 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
11 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
12 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
13 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
14 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
2 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
3 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
4 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
5 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
6 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
7 4R6E ic50 = 132 nM 3JD C19 H20 N4 O c1cc2cn(nc....
8 4ZZZ Kd = 0.087 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
9 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
10 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
11 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
12 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
13 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
14 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
15 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
16 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
17 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
18 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
19 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
20 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
21 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
22 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
23 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
24 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
25 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
26 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
27 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
28 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
29 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
30 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
31 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
32 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1WQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1WQ 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 4pjt.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4B1V LAB 0.01622 0.41768 1.89189
2 5LX9 OLB 0.02587 0.4003 2.11268
3 1M2Z BOG 0.01617 0.42773 2.33463
4 4UCC ZKW 0.03339 0.41238 2.57511
5 1TOX NAD 0.00001961 0.45392 2.7027
6 3G5K BB2 0.009333 0.41818 2.73224
7 1TV5 N8E 0.00811 0.45302 2.97297
8 5V4R MGT 0.00986 0.44955 3.08642
9 4H03 NAD 0.004602 0.43275 3.24324
10 4CJN QNZ 0.01695 0.42757 3.24324
11 4Z9D NAD 0.00007208 0.41272 3.42857
12 4KJU 1RH 0.03154 0.41333 3.48837
13 3Q9O NAD 0.000001273 0.47444 3.51351
14 1OG1 TAD 0.0003296 0.40107 3.53982
15 1G27 BB1 0.01694 0.40262 3.57143
16 3KU0 ADE 0.02493 0.42091 3.58566
17 1XK9 P34 0.0000008608 0.47852 3.72093
18 2G30 ALA ALA PHE 0.004989 0.4082 3.87597
19 3SE5 ANP 0.01641 0.40652 4.26829
20 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.03609 0.40355 4.91803
21 4YC0 5OF 0.00006185 0.42467 5.02092
22 2VDF OCT 0.002561 0.4435 5.13834
23 4RW3 PLM 0.01866 0.42333 5.29801
24 3ESS 18N 0.000000004721 0.42833 5.65217
25 2YPI PGA 0.03228 0.40239 6.47773
26 3B82 NAD 0.000003643 0.47024 6.48649
27 4MGA 27L 0.02397 0.42464 6.66667
28 2A5F NAD 0.00004458 0.40053 7.2973
29 4URN NOV 0.01658 0.42566 10.2222
30 1WS1 BB2 0.009529 0.41775 10.2564
31 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.01409 0.4208 11.4286
32 5OCA 9QZ 0.0003544 0.51043 12.6984
33 3KP6 SAL 0.02873 0.42141 13.245
34 5KAX RHQ 0.01832 0.42334 13.253
35 5TVM PUT 0.03889 0.40264 15.2941
Pocket No.: 2; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 4pjt.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4B1X LAB 0.007229 0.43329 1.89189
2 4IGH 1EA 0.0247 0.40138 2.7027
3 4IGH FMN 0.0247 0.40138 2.7027
4 4IGH ORO 0.0247 0.40138 2.7027
5 5UC9 MYR 0.03529 0.40507 4.86726
6 4XNV BUR 0.03644 0.40585 6.21622
7 2XG5 EC2 0.006696 0.43832 10.4046
8 2XG5 EC5 0.006696 0.43832 10.4046
9 2PSM BAM 0.003829 0.40745 14.1026
Pocket No.: 3; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 4pjt.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O1O RIS 0.03332 0.40355 3.80435
2 5AZC PGT 0.01841 0.41376 6
3 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.01167 0.40172 8
Pocket No.: 4; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found: 27
This union binding pocket(no: 4) in the query (biounit: 4pjt.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.002867 0.46136 None
2 3KO0 TFP 0.02035 0.42878 None
3 5UDS ATP 0.03059 0.40243 2.44755
4 4DR9 BB2 0.009344 0.41691 3.64583
5 4F4S EFO 0.03273 0.40861 3.94737
6 4XCP PLM 0.027 0.41399 4.11765
7 4RW3 TDA 0.04373 0.41528 5.29801
8 3TDC 0EU 0.02719 0.4323 5.94595
9 3KMR EQN 0.006772 0.41642 6.01504
10 4B7P 9UN 0.007102 0.40294 6.08696
11 3E3U NVC 0.02457 0.40023 6.09137
12 1RL4 BL5 0.0312 0.41569 6.38298
13 1XVB 3BR 0.004213 0.44613 6.47059
14 4MG8 27J 0.01808 0.40671 6.66667
15 2XCM ADP 0.02423 0.40052 6.75676
16 1J78 VDY 0.04005 0.40002 7.02703
17 2V5E SCR 0.009466 0.43847 7.92079
18 3I7V B4P 0.009297 0.40131 8.95522
19 1NF8 BOG 0.0075 0.45194 9.17874
20 3DGY 2GP 0.04451 0.4025 10.3093
21 1GEG GLC 0.0315 0.40252 12.5
22 2CB8 MYA 0.04386 0.40449 13.7931
23 2VWA PTY 0.001936 0.48671 13.8614
24 5JLB SAH 0.01725 0.40429 13.9785
25 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.007577 0.45625 14.966
26 1L0I PSR 0.02437 0.41718 17.9487
27 4IBF 1D5 0.004084 0.43795 18.6047
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