Receptor
PDB id Resolution Class Description Source Keywords
3QIN 1.7 Å EC: 3.4.23.16 CRYSTAL STRUCTURE OF HIV-1 RNASE H P15 WITH ENGINEERED E. CO AND PYRIMIDINOL CARBOXYLIC ACID INHIBITOR HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GRSUBTYPE B, ESCHERICHIA COLI (STRAIN K12), HUMAN IMMUNODEFICVIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE HXB2) RNASE H HIV-1 INHIBITOR NUCLEASE TRANSFERASE HYDROLASE-COMPLEX
Ref.: STRUCTURAL AND BINDING ANALYSIS OF PYRIMIDINOL CARB ACID AND N-HYDROXY QUINAZOLINEDIONE HIV-1 RNASE H INHIBITORS. ANTIMICROB.AGENTS CHEMOTHER. V. 55 2905 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:1;
A:2;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
P1Y A:700;
Valid;
none;
Kd = 136 nM
355.141 C13 H11 Br N2 O5 COc1c...
SO4 A:3;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3QIN 1.7 Å EC: 3.4.23.16 CRYSTAL STRUCTURE OF HIV-1 RNASE H P15 WITH ENGINEERED E. CO AND PYRIMIDINOL CARBOXYLIC ACID INHIBITOR HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GRSUBTYPE B, ESCHERICHIA COLI (STRAIN K12), HUMAN IMMUNODEFICVIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE HXB2) RNASE H HIV-1 INHIBITOR NUCLEASE TRANSFERASE HYDROLASE-COMPLEX
Ref.: STRUCTURAL AND BINDING ANALYSIS OF PYRIMIDINOL CARB ACID AND N-HYDROXY QUINAZOLINEDIONE HIV-1 RNASE H INHIBITORS. ANTIMICROB.AGENTS CHEMOTHER. V. 55 2905 2011
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 3QIN Kd = 136 nM P1Y C13 H11 Br N2 O5 COc1ccc(cc....
2 3HYF ic50 = 1.2 uM ON1 C12 H8 Cl2 N2 O4 c1cc(c(cc1....
3 3QIO Kd = 144 nM QID C14 H10 N2 O5 S c1ccc(cc1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3QIN Kd = 136 nM P1Y C13 H11 Br N2 O5 COc1ccc(cc....
2 3HYF ic50 = 1.2 uM ON1 C12 H8 Cl2 N2 O4 c1cc(c(cc1....
3 3QIO Kd = 144 nM QID C14 H10 N2 O5 S c1ccc(cc1)....
4 3K2P Kd = 6 uM JTH C10 H12 O3 CC(C)C1=CC....
5 4QAG ic50 = 4.8 uM F95 C11 H8 O6 c1cc(c(c2c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3QIN Kd = 136 nM P1Y C13 H11 Br N2 O5 COc1ccc(cc....
2 3HYF ic50 = 1.2 uM ON1 C12 H8 Cl2 N2 O4 c1cc(c(cc1....
3 3QIO Kd = 144 nM QID C14 H10 N2 O5 S c1ccc(cc1)....
4 3K2P Kd = 6 uM JTH C10 H12 O3 CC(C)C1=CC....
5 4QAG ic50 = 4.8 uM F95 C11 H8 O6 c1cc(c(c2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: P1Y; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 P1Y 1 1
2 ON1 0.560606 0.907407
Similar Ligands (3D)
Ligand no: 1; Ligand: P1Y; Similar ligands found: 67
No: Ligand Similarity coefficient
1 TCW 0.9281
2 LVE 0.9229
3 QC1 0.9166
4 0QX 0.9122
5 AX8 0.9091
6 PU2 0.9080
7 TOP 0.9034
8 7WD 0.9017
9 94M 0.9015
10 F0C 0.9013
11 J90 0.8997
12 M62 0.8969
13 8MF 0.8968
14 0RU 0.8954
15 50Q 0.8942
16 N1Y 0.8939
17 4P8 0.8935
18 AX4 0.8918
19 KUP 0.8913
20 R75 0.8907
21 CMP 0.8903
22 5AV 0.8900
23 C4F 0.8900
24 IM4 0.8888
25 4VT 0.8879
26 SCE 0.8873
27 GLA GAL 0.8847
28 12R 0.8826
29 XDH 0.8826
30 NOJ BGC 0.8822
31 IWH 0.8818
32 FKG 0.8808
33 EMU 0.8795
34 I0D 0.8794
35 INI 0.8791
36 TH4 0.8791
37 PNJ 0.8783
38 QTV 0.8777
39 JCQ 0.8772
40 7VV 0.8765
41 A4V 0.8759
42 5V3 0.8748
43 XDI 0.8742
44 5R9 0.8742
45 HN3 0.8741
46 D5F 0.8739
47 AEY 0.8736
48 MXA 0.8714
49 DE7 0.8710
50 LFK 0.8703
51 9ME 0.8697
52 GZT 0.8694
53 9FN 0.8684
54 RK4 0.8682
55 F91 0.8682
56 YX0 0.8676
57 ZEA 0.8675
58 D4X 0.8672
59 FEU 0.8634
60 BC3 0.8634
61 HHV 0.8633
62 6UW 0.8617
63 HN2 0.8614
64 6J7 0.8583
65 CC2 0.8540
66 QRP 0.8531
67 3AK 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QIN; Ligand: P1Y; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3qin.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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