Receptor
PDB id Resolution Class Description Source Keywords
4QD3 1.89 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM PSEUDOMONA AERUGINOSA WITH 5-AZACYTIDINE AT 1.89 ANGSTROM RESOLUTION PSEUDOMONAS AERUGINOSA HYDROLASE
Ref.: STRUCTURAL AND BINDING STUDIES OF PEPTIDYL-TRNA HYD FROM PSEUDOMONAS AERUGINOSA PROVIDE A PLATFORM FOR STRUCTURE-BASED INHIBITOR DESIGN AGAINST PEPTIDYL-T HYDROLASE BIOCHEM.J. V. 463 329 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5AE A:201;
Valid;
none;
Kd = 0.00000145 M
244.205 C8 H12 N4 O5 C1=NC...
GOL A:202;
Invalid;
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
4QBK 1.77 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDYL-TRNA HYDROLASE PSEUDOMONAS AERUGINOSA WITH AMINO ACYL-TRNA ANALOGUE AT 1.7R ESOLUTION PSEUDOMONAS AERUGINOSA PTH HYDROLASE
Ref.: STRUCTURAL AND BINDING STUDIES OF PEPTIDYL-TRNA HYD FROM PSEUDOMONAS AERUGINOSA PROVIDE A PLATFORM FOR STRUCTURE-BASED INHIBITOR DESIGN AGAINST PEPTIDYL-T HYDROLASE BIOCHEM.J. V. 463 329 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4QD3 Kd = 0.00000145 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
2 4QBK Kd = 0.00000145 M 3NZ C20 H25 N7 O5 COc1ccc(cc....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4JWK Kd = 5.3 nM CTN C9 H13 N3 O5 C1=CN(C(=O....
2 4JX9 Kd = 1.4 nM URI C9 H12 N2 O6 C1=CN(C(=O....
3 4QD3 Kd = 0.00000145 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
4 4QBK Kd = 0.00000145 M 3NZ C20 H25 N7 O5 COc1ccc(cc....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4JWK Kd = 5.3 nM CTN C9 H13 N3 O5 C1=CN(C(=O....
2 4JX9 Kd = 1.4 nM URI C9 H12 N2 O6 C1=CN(C(=O....
3 4QD3 Kd = 0.00000145 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
4 4QBK Kd = 0.00000145 M 3NZ C20 H25 N7 O5 COc1ccc(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5AE; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 5AE 1 1
2 CTN 0.542373 0.935484
3 AR3 0.542373 0.935484
4 F01 0.52459 0.865672
5 CTD 0.483333 0.854839
6 ZEB 0.419355 0.887097
7 U 0.412698 0.887097
8 URI 0.412698 0.887097
9 URD 0.412698 0.777778
10 DHZ 0.40625 0.887097
11 DKZ 0.405797 0.80597
12 5HM 0.405405 0.794521
13 5UD 0.4 0.820895
14 2TU 0.4 0.818182
15 BRD 0.4 0.83871
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4QBK; Ligand: 3NZ; Similar sites found: 24
This union binding pocket(no: 1) in the query (biounit: 4qbk.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5I2E 67D 0.04779 0.4056 None
2 5LNE A2G GAL 0.004282 0.43271 2.43902
3 5UGW GSH 0.004994 0.42168 2.85714
4 1J6W MET 0.01656 0.40141 2.85714
5 3AQT RCO 0.0152 0.40382 3.09278
6 2Q2Y ADP 0.0431 0.40293 3.09278
7 2Q2Y MKR 0.0414 0.40293 3.09278
8 2UYQ SAM 0.009215 0.41118 3.60825
9 1YKI NFZ 0.03621 0.40303 3.68664
10 1W3R PYR 0.01806 0.41336 4.63918
11 5H1W LER 0.009124 0.41659 5.6701
12 1R55 097 0.01208 0.40162 6.18557
13 3G4G D71 0.0081 0.4163 7.2165
14 3BQD DAY 0.01116 0.4131 7.73196
15 1QM5 PLP 0.04872 0.40515 7.73196
16 1QM5 GLC GLC GLC PO4 SGC GLC 0.03574 0.40333 7.73196
17 4P6X HCY 0.01778 0.40151 7.73196
18 3B9Z CO2 0.01652 0.41732 8.24742
19 1PZX PLM 0.01822 0.40266 9.79381
20 2Z9I GLY ALA THR VAL 0.01497 0.40533 10.3093
21 1SR7 MOF 0.02343 0.40952 12.3711
22 2PHF MAN MAN BMA MAN 0.009083 0.40759 12.6984
23 2PHR MAN MAN BMA MAN 0.009318 0.40705 12.6984
24 3AD8 NAD 0.03793 0.40198 25.2525
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