Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:201;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
3NZ A:202;
Valid;
none;
Kd = 0.00000145 M
443.456 C20 H25 N7 O5 COc1c...
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: 3NZ; Similar ligands found: 107
No: Ligand ECFP6 Tc MDL keys Tc
1 3NZ 1 1
2 D3Y 0.827586 0.956522
3 A3S 0.701149 0.927536
4 A3T 0.648352 0.913043
5 A3G 0.588889 0.914286
6 YSA 0.522523 0.747126
7 VRT 0.5 0.902778
8 2VA 0.485149 0.887324
9 YAP 0.473684 0.833333
10 SO8 0.471154 0.875
11 5X8 0.470588 0.847222
12 LSS 0.45045 0.711111
13 XYA 0.449438 0.884058
14 RAB 0.449438 0.884058
15 ADN 0.449438 0.884058
16 6RE 0.44898 0.792208
17 EEM 0.448598 0.807692
18 FA5 0.448276 0.820513
19 AHX 0.446429 0.8125
20 A3P 0.445545 0.75641
21 A5A 0.444444 0.712644
22 3AM 0.443299 0.766234
23 SSA 0.440367 0.747126
24 SMM 0.440367 0.8
25 5N5 0.43956 0.857143
26 AMP 0.438776 0.779221
27 A 0.438776 0.779221
28 DSZ 0.4375 0.727273
29 VMS 0.436364 0.696629
30 54H 0.436364 0.696629
31 EP4 0.43617 0.810811
32 5AL 0.435185 0.794872
33 A4D 0.434783 0.857143
34 FYA 0.434783 0.818182
35 5CD 0.434783 0.816901
36 SA8 0.433962 0.828947
37 53H 0.432432 0.688889
38 5CA 0.432432 0.747126
39 TSB 0.432432 0.724138
40 M2T 0.431579 0.789474
41 NEC 0.43 0.830986
42 SFG 0.428571 0.833333
43 WSA 0.427419 0.735632
44 S7M 0.427273 0.78481
45 SRP 0.427273 0.820513
46 MTA 0.427083 0.833333
47 5AD 0.426966 0.782609
48 GSU 0.426087 0.707865
49 SAM 0.425926 0.807692
50 J7C 0.425743 0.802632
51 ABM 0.425743 0.805195
52 0UM 0.424779 0.818182
53 AMO 0.424779 0.820513
54 52H 0.423423 0.688889
55 SON 0.423077 0.775
56 7D5 0.42268 0.725
57 NB8 0.422414 0.790123
58 7D7 0.422222 0.777778
59 GJV 0.421569 0.782051
60 7MD 0.421488 0.783133
61 DLL 0.421053 0.794872
62 PAP 0.420561 0.769231
63 TYR AMP 0.420168 0.820513
64 CA0 0.419048 0.78481
65 3DH 0.418367 0.808219
66 G5A 0.416667 0.727273
67 DTA 0.416667 0.797297
68 SAI 0.416667 0.813333
69 SAH 0.416667 0.824324
70 8QN 0.415929 0.794872
71 AMP MG 0.415842 0.759494
72 KAA 0.413793 0.703297
73 ADP 0.413462 0.782051
74 5AS 0.413462 0.688889
75 GAP 0.412844 0.78481
76 PAJ 0.412281 0.780488
77 A2D 0.411765 0.805195
78 PRX 0.411215 0.7625
79 ME8 0.410256 0.783133
80 AN2 0.409524 0.772152
81 PPS 0.409091 0.689655
82 NVA LMS 0.408696 0.692308
83 XAH 0.408333 0.761905
84 DAL AMP 0.40708 0.794872
85 KB1 0.40678 0.794872
86 OVE 0.405941 0.75
87 SRA 0.405941 0.740741
88 AU1 0.40566 0.7625
89 M33 0.40566 0.818182
90 LEU LMS 0.405172 0.692308
91 2AM 0.40404 0.779221
92 BA3 0.403846 0.805195
93 A12 0.403846 0.775
94 AP2 0.403846 0.775
95 AOC 0.401961 0.833333
96 ACP 0.401869 0.78481
97 ATP 0.401869 0.782051
98 LAD 0.401709 0.780488
99 WAQ 0.401709 0.756098
100 YLC 0.401575 0.783133
101 YLB 0.401575 0.764706
102 NSS 0.4 0.727273
103 B4P 0.4 0.805195
104 AP5 0.4 0.805195
105 ACQ 0.4 0.78481
106 4AD 0.4 0.810127
107 YLP 0.4 0.764706
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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