-->
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...
View in 3D viewer
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 16 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 13 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 (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5XSU ic50 = 244 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 ic50 = 17 nM 8EC C15 H13 F N4 O S c1c(cc2c(c....
5 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
6 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
7 4HHY ic50 = 0.0019 uM 15R C33 H30 F N5 O4 c1ccc2c(c1....
8 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
9 5XST ic50 = 27 nM 8E6 C15 H13 F N4 O S c1c(cc2c(c....
10 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
11 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
12 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
13 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
14 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
15 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
16 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
17 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
18 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
19 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
20 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
21 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
22 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
23 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
24 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
25 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
26 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
27 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
28 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
29 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
30 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
31 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
32 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
33 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
34 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
35 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
36 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
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 with APoc: 100
This union binding pocket(no: 1) in the query (biounit: 3kjd.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 1UO5 PIH None
3 4WG0 CHD None
4 2ZWS PLM 1.63043
5 1SBR VIB 1.63043
6 2WN6 NDP 1.72786
7 4FXQ G9L 1.90217
8 4M3P HCS 1.90217
9 4WOE ADP 1.90217
10 4WMY 3S6 1.96078
11 1QDS PGA 1.99203
12 4GK9 MAN BMA MAN MAN MAN 2.15054
13 2Z49 AMG 2.17391
14 3QX9 ATP 2.17391
15 5N9X THR 2.71739
16 4MG9 27K 2.7451
17 3Q9O NAD 2.98913
18 4QO5 NAG 2.98913
19 1VRP IOM 2.98913
20 3B99 U51 2.98913
21 3JQ8 DX3 3.125
22 3GD8 GOL 3.13901
23 4RF7 ARG 3.26087
24 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 3.26087
25 4Z9D NAD 3.42857
26 6FA4 D1W 3.46821
27 1VEM GLC GLC 3.53261
28 3H0L ADP 3.53261
29 3KP6 SAL 3.53261
30 3QPB URA 3.5461
31 5DZ2 212 3.5503
32 6BVM EBV 3.59281
33 6BVK EAV 3.59281
34 6BVJ EAS 3.59281
35 6BVL EBY 3.59281
36 6BVI EC4 3.59281
37 1DTP APU 3.68421
38 6CB2 OLC 3.80435
39 4ZH7 FUC GAL NAG GAL FUC 3.80435
40 4OJP MAL 3.80435
41 1JPA ANP 3.84615
42 1YOK P6L 3.90625
43 2VDF OCT 3.95257
44 5NE2 DGL 3.95683
45 4FK7 P34 4.07609
46 3TW1 AHN 4.21941
47 5OCG 9R5 4.2328
48 4YC0 5OF 4.34783
49 2HZL PYR 4.38356
50 2YPI PGA 4.45344
51 1XK9 P34 4.65116
52 1GZF NIR 4.73934
53 1GZF ADP 4.73934
54 1GZF NAD 4.73934
55 3ESS 18N 4.78261
56 3B82 NAD 4.83092
57 3E7W AMP 4.8913
58 4UBS DIF 4.8913
59 4LI4 AMP 5.14706
60 3I7V B4P 5.22388
61 4LO6 SIA GAL 5.26316
62 1GPM AMP 5.43478
63 1OG1 TAD 5.75221
64 4K7O EKZ 5.95238
65 1Q7E MET 5.97826
66 1TOX NAD 6.25
67 5MLJ 9ST 6.25
68 4CSD MFU 6.25
69 6A0S NDP 6.3253
70 5EWK P34 6.5
71 5YW5 ADE 6.70391
72 2BVE PH5 6.72269
73 5NM7 GLY 6.76692
74 4MRP GSH 7.06522
75 5VKM GAL SIA 7.09877
76 1QV1 CZH 7.17949
77 4URX FK1 7.56757
78 1G51 AMP 7.93103
79 1QKQ MAN 8.4507
80 1PVC ILE SER GLU VAL 8.63787
81 5ZJ5 NAI 8.64198
82 5DYO FLU 8.7156
83 4C2W ANP 9.67742
84 4H03 NAD 10.0543
85 1T0S BML 10.4651
86 5YSI NCA 10.5263
87 1RV1 IMZ 10.5882
88 2A9K NAD 11.2299
89 3RV5 DXC 11.236
90 2XG5 EC5 11.4679
91 2XG5 EC2 11.4679
92 2A5F NAD 12.4352
93 5W97 CHD 15.0685
94 5Z84 CHD 15.0685
95 5ZCO CHD 15.0685
96 5FUI APY 15.1515
97 2W5P CL8 16.7785
98 5EW9 5VC 16.9742
99 1XTT U5P 19.9074
100 5W7B MYR 26.2411
Pocket No.: 2; Query (leader) PDB : 3KJD; Ligand: 78P; Similar sites found with APoc: 21
This union binding pocket(no: 2) in the query (biounit: 3kjd.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1RYD GLC 1.08696
2 4YJK URA 1.98413
3 5VLQ ANP 2.17391
4 4CJN QNZ 2.71739
5 4TV1 36M 2.78884
6 5H04 NAI 2.98913
7 1NW4 IMH 3.62319
8 3KVY URA 3.8835
9 5U5G 7VD 4.0678
10 4U60 SIA 4.28571
11 6F5W KG1 5.42005
12 4U8P UDP 5.45809
13 1RJW ETF 5.60472
14 5IFK HPA 6.41026
15 6F4W FMC 6.43777
16 5C9P FUC 6.52174
17 6C5F 7L9 6.83761
18 2XOM GAL GAL GAL 8.55263
19 5KJW 53C 11.9565
20 5ZWP GSH 13.4615
21 2G30 ALA ALA PHE 43.75
APoc FAQ
Feedback