Receptor
PDB id Resolution Class Description Source Keywords
4JWK 1.87 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDYL-TRNA HYDROLASE ACINETOBACTER BAUMANNII WITH CYTIDINE AT 1.87 A RESOLUTION ACINETOBACTER BAUMANNII ATCC 19606 = CORGANISM_TAXID: 575584 PROTEIN SYNTHESIS COMPLEX HYDROLASE
Ref.: THE MODE OF INHIBITOR BINDING TO PEPTIDYL-TRNA HYDR BINDING STUDIES AND STRUCTURE DETERMINATION OF UNBO BOUND PEPTIDYL-TRNA HYDROLASE FROM ACINETOBACTER BA PLOS ONE V. 8 67547 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CTN A:201;
Valid;
none;
Kd = 5.3 nM
243.217 C9 H13 N3 O5 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JWK 1.87 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDYL-TRNA HYDROLASE ACINETOBACTER BAUMANNII WITH CYTIDINE AT 1.87 A RESOLUTION ACINETOBACTER BAUMANNII ATCC 19606 = CORGANISM_TAXID: 575584 PROTEIN SYNTHESIS COMPLEX HYDROLASE
Ref.: THE MODE OF INHIBITOR BINDING TO PEPTIDYL-TRNA HYDR BINDING STUDIES AND STRUCTURE DETERMINATION OF UNBO BOUND PEPTIDYL-TRNA HYDROLASE FROM ACINETOBACTER BA PLOS ONE V. 8 67547 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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....
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: CTN; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 CTN 1 1
2 AR3 1 1
3 I5A 0.754717 0.920635
4 DKZ 0.719298 0.863636
5 CAR 0.672131 0.842857
6 C 0.672131 0.842857
7 C5P 0.672131 0.842857
8 C3P 0.655738 0.828571
9 CDP 0.636364 0.857143
10 CTP 0.608696 0.857143
11 C2P 0.603175 0.842857
12 CDP MG 0.57971 0.819444
13 7XL 0.575342 0.859155
14 C2G 0.552632 0.871429
15 CTD 0.551724 0.887097
16 C5G 0.55 0.859155
17 5AE 0.542373 0.935484
18 GEO 0.532258 0.878788
19 C C 0.525641 0.842857
20 DCZ 0.52459 0.907692
21 LDC 0.52459 0.907692
22 CDM 0.518519 0.813333
23 F01 0.516129 0.924242
24 CDC 0.506173 0.728395
25 U 0.5 0.919355
26 URI 0.5 0.919355
27 CSQ 0.494253 0.821918
28 CSV 0.494253 0.821918
29 CXY 0.488095 0.833333
30 NVG 0.476744 0.810811
31 URD 0.47541 0.809524
32 V12 0.470588 0.833333
33 2TU 0.460317 0.848485
34 CJB 0.453125 0.873016
35 LTT 0.453125 0.876923
36 CC7 0.452055 0.802817
37 3TC 0.446154 0.835821
38 1AA 0.445652 0.8
39 16B 0.444444 0.783784
40 ZEB 0.435484 0.919355
41 G C 0.427184 0.759494
42 DC 0.424658 0.756757
43 DCM 0.424658 0.756757
44 DHZ 0.421875 0.919355
45 BRD 0.415385 0.870968
46 GPC 0.415094 0.722892
47 PMT 0.41 0.75
48 MCN 0.403846 0.722892
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JWK; Ligand: CTN; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 4jwk.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZFU SAH 0.02239 0.41014 None
2 4XB2 HSE 0.01974 0.4207 1.5544
3 4XB2 NDP 0.01279 0.4207 1.5544
4 5G3U ITW 0.01146 0.44989 2.07254
5 1KZN CBN 0.009333 0.4269 2.07254
6 4CFP NAG AMU NAG AMV 0.02298 0.4105 2.07254
7 2LBD REA 0.004352 0.4495 2.59067
8 4N9I PCG 0.03492 0.41879 2.59067
9 1CF2 NAP 0.02631 0.40748 2.59067
10 1QM5 GLC GLC GLC PO4 SGC GLC 0.04015 0.40607 2.59067
11 5M58 SAH 0.03016 0.40293 2.59067
12 3CEV ARG 0.03693 0.40186 2.59067
13 3NC9 TR3 0.03033 0.41731 3.10881
14 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 0.01633 0.41413 3.10881
15 4BAE RWX 0.01167 0.40947 3.10881
16 4PIV 2W4 0.0175 0.40875 3.10881
17 2PHX MAN MAN MAN MAN 0.01007 0.40597 3.10881
18 1Q8V MAN MAN MAN 0.01129 0.40402 3.10881
19 3DRW AMP 0.01533 0.40135 3.10881
20 1CX4 CMP 0.005521 0.43259 3.62694
21 4HA9 NDP 0.02264 0.40369 3.62694
22 1YC5 NCA 0.03285 0.40015 4.14508
23 3FRH SAH 0.0287 0.40237 4.34783
24 2WCU FUC 0.007503 0.40545 4.69799
25 2REG CHT 0.004011 0.41599 7.77202
26 3BQD DAY 0.0245 0.40338 7.77202
27 5FXD H7Y 0.02195 0.4024 8.29016
28 3I59 N6R 0.008155 0.42645 9.32642
29 1RE8 BD2 0.03338 0.41898 9.32642
30 5BO9 CSF 0.02751 0.40436 9.32642
31 5T67 SAH 0.04553 0.41198 10.3627
32 5L95 AMP 0.02114 0.40475 10.3627
33 4WW7 AMP 0.02613 0.40157 10.8808
34 1SR7 MOF 0.04194 0.40567 12.9534
35 4P6X HCY 0.007722 0.42952 14.5078
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