Receptor
PDB id Resolution Class Description Source Keywords
3QIN 1.7 Å EC: 3.1.26.4 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: 3.1.26.4 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 3 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 2 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 2 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
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 Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QIN; Ligand: P1Y; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 3qin.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YUC EPH 0.03613 0.40106 None
2 3ASZ C5P 0.005123 0.43735 2.66667
3 3UMV FAD 0.03143 0.40396 2.66667
4 3A51 VDY 0.0147 0.40277 2.66667
5 1Z41 FMN 0.0386 0.40312 2.95858
6 1GRN GDP 0.01879 0.40467 3.33333
7 1RM6 PCD 0.02009 0.4217 4
8 4CRL C1I 0.009366 0.4271 4.66667
9 1TUF AZ1 0.01591 0.42303 4.66667
10 3PB9 1BN 0.005723 0.40817 4.66667
11 1N62 MCN 0.0345 0.40374 4.66667
12 3GF4 FAD 0.02682 0.42855 5.33333
13 3GF4 UPG 0.04253 0.42093 5.33333
14 3C56 PH4 0.03211 0.40676 6
15 2W2X GSP 0.01771 0.41026 6.45161
16 2ZJ1 ARJ 0.03639 0.42154 7.33333
17 4YC7 GNP 0.02387 0.40182 7.33333
18 1TKB N1T 0.03995 0.401 7.33333
19 3MTW M3R 0.003679 0.44344 8.66667
20 3PF7 MLA 0.03817 0.40542 8.66667
21 2GAG FAD 0.03994 0.42003 9.09091
22 2GAG FOA 0.03994 0.42003 9.09091
23 3AMN CBK 0.02175 0.41163 9.33333
24 3AMN CBI 0.02175 0.41163 9.33333
25 4KVL PLM 0.02206 0.40278 9.33333
26 1EWF PC1 0.03697 0.40204 9.33333
27 4YSX FAD 0.04475 0.40478 10
28 2CJA ATP 0.02109 0.41735 11.3333
29 3GAY P6T 0.0228 0.41349 11.3333
30 3ZJ0 ACO 0.02593 0.40531 12
31 5GUE GGS 0.02688 0.40061 12
32 4D8N 0HM 0.01605 0.42173 14
33 3PBB PBD 0.007824 0.41873 14
34 4IV9 FAD 0.03834 0.40252 19.3333
35 1U26 IHS 0.01349 0.40083 19.3333
36 1O69 X04 0.04475 0.40528 28.6667
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