Receptor
PDB id Resolution Class Description Source Keywords
3KJD 1.95 Å EC: 2.4.2.30 HUMAN POLY(ADP-RIBOSE) POLYMERASE 2, CATALYTIC FRAGMENT IN C WITH AN INHIBITOR ABT-888 HOMO SAPIENS TRANSFERASE ENZYME-INHIBITOR COMPLEX CATALYTIC FRAGMENT SGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC GLYCOSYLTRANNAD NUCLEUS DNA-BINDING
Ref.: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEX WITH PARP INHIBITOR ABT-888. BIOCHEMISTRY V. 49 1056 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
78P A:1;
B:1;
Valid;
Valid;
none;
none;
Kd = 2.9 nM
244.292 C13 H16 N4 O C[C@@...
GOL A:580;
B:2;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KJD 1.95 Å EC: 2.4.2.30 HUMAN POLY(ADP-RIBOSE) POLYMERASE 2, CATALYTIC FRAGMENT IN C WITH AN INHIBITOR ABT-888 HOMO SAPIENS TRANSFERASE ENZYME-INHIBITOR COMPLEX CATALYTIC FRAGMENT SGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC GLYCOSYLTRANNAD NUCLEUS DNA-BINDING
Ref.: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEX WITH PARP INHIBITOR ABT-888. BIOCHEMISTRY V. 49 1056 2010
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 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....
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: 78P; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 78P 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KJD; Ligand: 78P; Similar sites found: 43
This union binding pocket(no: 1) in the query (biounit: 3kjd.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.03303 0.40219 None
2 2ZWS PLM 0.01883 0.4312 1.63043
3 2WN6 NDP 0.002354 0.43853 1.72786
4 4WOE ADP 0.02253 0.40967 1.90217
5 4GK9 MAN BMA MAN MAN MAN 0.01075 0.43108 2.15054
6 5N9X THR 0.01686 0.41136 2.71739
7 3Q9O NAD 0.000007087 0.52469 2.98913
8 1VRP IOM 0.008084 0.42021 2.98913
9 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.01578 0.41739 3.26087
10 4Z9D NAD 0.0007082 0.42291 3.42857
11 3KP6 SAL 0.02356 0.41527 3.53261
12 1DTP APU 0.001997 0.40845 3.68421
13 1GMN IDS SGN IDS SGN IDS 0.02747 0.40617 3.82514
14 1JPA ANP 0.01862 0.40497 3.84615
15 1YOK P6L 0.01221 0.40178 3.90625
16 2VDF OCT 0.001294 0.4638 3.95257
17 5NE2 DGL 0.02602 0.41358 3.95683
18 4AZT LY2 0.01846 0.40398 4.07609
19 3TW1 AHN 0.02269 0.40874 4.21941
20 4YC0 5OF 0.00014 0.46596 4.34783
21 2YPI PGA 0.02089 0.40133 4.45344
22 1XK9 P34 0.000002441 0.53091 4.65116
23 1GZF NIR 0.0008205 0.48219 4.73934
24 1GZF ADP 0.003522 0.4223 4.73934
25 1GZF NAD 0.006066 0.40489 4.73934
26 3ESS 18N 0.00000004576 0.46838 4.78261
27 3B82 NAD 0.000004968 0.5155 4.83092
28 3I7V B4P 0.00876 0.40068 5.22388
29 1OG1 TAD 0.0001675 0.45733 5.75221
30 1TOX NAD 0.000007173 0.42886 6.25
31 5EWK P34 0.0001699 0.52157 6.5
32 2BVE PH5 0.01456 0.40337 6.72269
33 4MRP GSH 0.01942 0.42265 7.06522
34 1VPD TLA 0.01039 0.4349 7.69231
35 1QKQ MAN 0.019 0.43202 8.4507
36 1PVC ILE SER GLU VAL 0.000648 0.47173 8.63787
37 4H03 NAD 0.003849 0.42446 10.0543
38 2A9K NAD 0.003819 0.41014 11.2299
39 2XG5 EC2 0.02409 0.40672 11.4679
40 2XG5 EC5 0.02409 0.40672 11.4679
41 2A5F NAD 0.0001379 0.49605 12.4352
42 5FUI APY 0.01945 0.41379 15.1515
43 2W5P CL8 0.02541 0.40641 16.7785
Pocket No.: 2; Query (leader) PDB : 3KJD; Ligand: 78P; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 3kjd.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CJN QNZ 0.01205 0.42657 2.71739
2 5U5G 7VD 0.02054 0.41144 4.0678
3 4U60 SIA 0.03568 0.40201 4.28571
4 5UDS ATP 0.01751 0.40666 5.24476
5 5XVK 8GC 0.03359 0.40125 5.28169
6 5IFK HPA 0.03649 0.40183 6.41026
7 2G30 ALA ALA PHE 0.003761 0.40598 43.75
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