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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2YQ B:1105;
C:1104;
D:1104;
A:1105;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 0.57 nM
380.351 C19 H14 F2 N6 O Cn1c(...
SO4 C:1101;
C:1103;
D:1101;
B:1104;
A:1104;
C:1102;
B:1103;
A:1101;
B:1106;
D:1103;
B:1101;
B:1102;
A:1103;
D:1102;
A:1102;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GOL C:1105;
A:1106;
A:1107;
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
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 (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 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....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 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 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
14 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
15 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
16 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
17 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
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: 2YQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 2YQ 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 with APoc: 149
This union binding pocket(no: 1) in the query (biounit: 4pjt.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4V1F BQ1 None
2 5O0J 8BR 1.35135
3 5CX8 TG6 1.62162
4 5WBF LAC 1.85185
5 1M0W ANP 1.89189
6 5OM2 DXT 1.89702
7 5LX9 OLB 2.11268
8 5KL0 G16 2.16216
9 2GSU AMP 2.16216
10 4LSJ LSJ 2.32558
11 1M2Z BOG 2.33463
12 4V3I ASP LEU THR ARG PRO 2.33463
13 6B21 C9V 2.43243
14 3B99 U51 2.43243
15 6C5F 7L9 2.5641
16 1RYD GLC 2.58398
17 1TOX NAD 2.7027
18 1OFL NGK GCD 2.7027
19 2BTM PGA 2.77778
20 4G86 BNT 2.8169
21 5UGW GSH 2.85714
22 4GK9 MAN BMA MAN MAN MAN 2.86738
23 1E4I NFG 2.97297
24 4RF7 ARG 2.97297
25 4UBS DIF 2.97297
26 1TV5 N8E 2.97297
27 2BHW NEX 3.01724
28 5V3Y 5V8 3.14685
29 4H03 NAD 3.24324
30 4CJN QNZ 3.24324
31 5FPN KYD 3.24324
32 3EVF GTA 3.2491
33 4WMY 3S6 3.26797
34 5ZDN CDP 3.31754
35 1YYE 196 3.35821
36 1YC4 43P 3.40909
37 4Z9D NAD 3.42857
38 4KJU 1RH 3.48837
39 3Q9O NAD 3.51351
40 5H04 NAI 3.51351
41 1OG1 TAD 3.53982
42 3KU0 ADE 3.58566
43 1DTP APU 3.68421
44 1XK9 P34 3.72093
45 1GZF NIR 3.79147
46 1GZF ADP 3.79147
47 1GZF NAD 3.79147
48 2G30 ALA ALA PHE 3.87597
49 4WGF HX2 3.90244
50 4EOY ASN ASP TRP LEU LEU PRO SER TYR 3.90625
51 4F4S EFO 3.94737
52 1QDS PGA 3.98406
53 5IUY BOG 4.05405
54 5URY PAM 4.10959
55 1G51 AMP 4.32432
56 6DIO CIT 4.32432
57 3E7S AT2 4.32432
58 4PTN GXV 4.32432
59 5XNA SHV 4.34783
60 6EGU 43Y 4.59459
61 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 4.60251
62 2W5P CL8 4.69799
63 3NB0 G6P 4.82759
64 5VKM GAL SIA 4.93827
65 1SBR VIB 5
66 4YC0 5OF 5.02092
67 4OWK NGA 5.07246
68 2VDF OCT 5.13834
69 5Z3I ADE 5.28302
70 4RW3 PLM 5.29801
71 6E1Q CFA 5.40541
72 5C9P FUC 5.40541
73 5EWK P34 5.5
74 2BP1 FLC 5.55556
75 3ESS 18N 5.65217
76 1OJZ NAD 5.66038
77 4FXQ G9L 5.67568
78 1Q1Y BB2 5.75916
79 5AOG IAC 5.86319
80 5UC4 83S 5.90909
81 2WN6 NDP 5.94595
82 5KJW 53C 5.94595
83 5AZC PGT 6
84 3KMR EQN 6.01504
85 3QPB URA 6.02837
86 5DYO FLU 6.13208
87 2A9K NAD 6.41711
88 1XVB 3BR 6.47059
89 2YPI PGA 6.47773
90 3B82 NAD 6.48649
91 5WGD EST 6.51341
92 5DXE EST 6.51341
93 5WGQ EST 6.51341
94 5HYR EST 6.58915
95 2QA8 GEN 6.58915
96 2QZO KN1 6.58915
97 6D28 NEC 6.59341
98 4TUZ 36J 6.66667
99 4MG8 27J 6.66667
100 4MG7 27H 6.66667
101 4MGA 27L 6.66667
102 1HK8 DGT 6.75676
103 3UUD EST 6.77291
104 4TV1 36M 6.77291
105 1SQL GUN 6.84932
106 2WOR 2AN 7
107 2J9L ATP 7.02703
108 4OGQ 7PH 7.26257
109 4OGQ UMQ 7.26257
110 2A5F NAD 7.2973
111 6BTQ E8S 7.42574
112 6C0B PAM 7.69231
113 1HBK MYR 7.86517
114 2V5E SCR 7.92079
115 2BCG GER 8.25243
116 1PVC ILE SER GLU VAL 8.30565
117 4FK7 P34 9.17031
118 1NF8 BOG 9.17874
119 1JG3 VAL TYR PRO IAS HIS ALA 9.3617
120 3QX9 ATP 9.42029
121 4OKD GLC GLC GLC 9.45946
122 4ZH7 FUC GAL NAG GAL FUC 9.72973
123 4MRP GSH 10
124 1OFU GDP 10.084
125 4URN NOV 10.2222
126 2XG5 EC5 10.4046
127 2XG5 EC2 10.4046
128 3OLL EST 10.5263
129 3QH2 3NM 10.8597
130 5WHT SIA GAL 10.8696
131 5WHT SIA 10.8696
132 5ZJ5 NAI 11.1111
133 5C9J STE 12.1212
134 5C9J DAO 12.1212
135 5OCA 9QZ 12.6984
136 5ZCO PGV 12.766
137 2DYR PGV 12.766
138 2DYS PGV 12.766
139 1T0S BML 12.7907
140 5YSI NCA 13.1579
141 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 14.966
142 4XSH NAI 15.5251
143 4RHS SIA SIA GAL 16.3934
144 6FA4 D1W 16.763
145 1L0I PSR 17.9487
146 4IBF 1D5 18.6047
147 1DTL BEP 18.6335
148 5LWY OLB 21.0084
149 6CB2 OLC 21.843
Pocket No.: 2; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 4pjt.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU None
2 3KVY URA 1.62162
3 5IFK HPA 2.5641
4 5EXK 5AD 3.02115
5 1M2T ADE 3.14961
6 3SBZ MLI 3.1746
7 5H4S RAM 3.87324
8 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 4.52381
9 4U8P UDP 4.59459
10 1GPM AMP 4.59459
11 2MJP ANP 4.66321
12 4YJK URA 4.7619
13 5YW5 ADE 5.58659
14 1PWB GLC 5.64972
15 3P3Z P3Z 5.67568
16 3I7V B4P 8.95522
17 1R6N 434 10.9005
18 4LO6 SIA GAL 12.4324
19 1USF NAP 14.6067
20 6GMN F4E 28.8462
Pocket No.: 3; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 14
This union binding pocket(no: 3) in the query (biounit: 4pjt.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 3KO0 TFP None
2 1UUO BRF 2.16216
3 4CSD MFU 2.20588
4 1QCI ADE 2.67176
5 2F6U CIT 2.99145
6 2XOM GAL GAL GAL 3.28947
7 5ZZB LAB 4.41176
8 5C1M OLC 4.8
9 6GR0 F8W 5.74713
10 2CIX CEJ 6.35452
11 2FKA BEF 6.97674
12 5YJS SAL 8.64865
13 3CBC DBS 11.6162
14 4WOE ADP 12.973
Pocket No.: 4; Query (leader) PDB : 4PJT; Ligand: 2YQ; Similar sites found with APoc: 29
This union binding pocket(no: 4) in the query (biounit: 4pjt.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 4WG0 CHD None
3 5N8V KZZ None
4 4V36 LYN 1.49254
5 6B04 C6J 2.34604
6 1SW0 PGA 2.41935
7 5XJ7 87O 2.98507
8 6FU4 HSM 3.18841
9 4F06 PHB 3.24324
10 4DDY DN6 3.42205
11 2O1O RIS 3.80435
12 2YJD YJD 4.05405
13 1ND4 KAN 4.54545
14 4I90 CHT 4.62046
15 3GF2 SAL 4.79452
16 5BOE PEP 4.86486
17 3TW1 AHN 5.06329
18 6BR8 6OU 5.15873
19 3TDC 0EU 5.94595
20 4Q0A 4OA 5.96026
21 3LE7 ADE 8.81226
22 3KP6 SAL 13.245
23 2CB8 MYA 13.7931
24 2VWA PTY 13.8614
25 5JLB SAH 13.9785
26 5OCG 9R5 15.3439
27 2GJ5 VD3 15.4321
28 3GWN FAD 16.6667
29 1EJH M7G 43.75
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