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: 120
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 J4G 0.561905 0.7875
7 YSA 0.522523 0.747126
8 VRT 0.5 0.902778
9 2VA 0.485149 0.887324
10 YAP 0.473684 0.833333
11 SO8 0.471154 0.875
12 5X8 0.470588 0.847222
13 NVA 2AD 0.461538 0.890411
14 LSS 0.45045 0.711111
15 ADN 0.449438 0.884058
16 XYA 0.449438 0.884058
17 RAB 0.449438 0.884058
18 6RE 0.44898 0.792208
19 EEM 0.448598 0.807692
20 FA5 0.448276 0.820513
21 AHX 0.446429 0.8125
22 A3P 0.445545 0.75641
23 A5A 0.444444 0.712644
24 3AM 0.443299 0.766234
25 SSA 0.440367 0.747126
26 SMM 0.440367 0.8
27 5N5 0.43956 0.857143
28 AMP 0.438776 0.779221
29 A 0.438776 0.779221
30 DSZ 0.4375 0.727273
31 54H 0.436364 0.696629
32 VMS 0.436364 0.696629
33 EP4 0.43617 0.810811
34 5AL 0.435185 0.794872
35 A4D 0.434783 0.857143
36 5CD 0.434783 0.816901
37 FYA 0.434783 0.818182
38 SA8 0.433962 0.828947
39 53H 0.432432 0.688889
40 TSB 0.432432 0.724138
41 5CA 0.432432 0.747126
42 M2T 0.431579 0.789474
43 NEC 0.43 0.830986
44 SFG 0.428571 0.833333
45 9ZA 0.428571 0.777778
46 9ZD 0.428571 0.777778
47 WSA 0.427419 0.735632
48 S7M 0.427273 0.78481
49 SRP 0.427273 0.820513
50 MTA 0.427083 0.833333
51 5AD 0.426966 0.782609
52 GSU 0.426087 0.707865
53 SAM 0.425926 0.807692
54 J7C 0.425743 0.802632
55 ABM 0.425743 0.805195
56 45A 0.425743 0.805195
57 0UM 0.424779 0.818182
58 AMO 0.424779 0.820513
59 52H 0.423423 0.688889
60 SON 0.423077 0.775
61 7D5 0.42268 0.725
62 NB8 0.422414 0.790123
63 7D7 0.422222 0.777778
64 GJV 0.421569 0.782051
65 7MD 0.421488 0.783133
66 DLL 0.421053 0.794872
67 PAP 0.420561 0.769231
68 8LQ 0.419643 0.797468
69 CA0 0.419048 0.78481
70 3DH 0.418367 0.808219
71 DTA 0.416667 0.797297
72 SAI 0.416667 0.813333
73 G5A 0.416667 0.727273
74 TYR AMP 0.416667 0.833333
75 SAH 0.416667 0.824324
76 8QN 0.415929 0.794872
77 N5O 0.415842 0.873239
78 KG4 0.415094 0.78481
79 8LH 0.414414 0.797468
80 KAA 0.413793 0.703297
81 ADP 0.413462 0.782051
82 5AS 0.413462 0.688889
83 GAP 0.412844 0.78481
84 PAJ 0.412281 0.780488
85 A2D 0.411765 0.805195
86 PRX 0.411215 0.7625
87 ME8 0.410256 0.783133
88 LMS 0.41 0.689655
89 AN2 0.409524 0.772152
90 PPS 0.409091 0.689655
91 8LE 0.409091 0.765432
92 NVA LMS 0.408696 0.703297
93 XAH 0.408333 0.761905
94 N5A 0.407767 0.84507
95 DAL AMP 0.40708 0.794872
96 KB1 0.40678 0.794872
97 OVE 0.405941 0.75
98 SRA 0.405941 0.740741
99 AU1 0.40566 0.7625
100 M33 0.40566 0.818182
101 LEU LMS 0.405172 0.703297
102 2AM 0.40404 0.779221
103 A12 0.403846 0.775
104 AP2 0.403846 0.775
105 BA3 0.403846 0.805195
106 HZ2 0.403226 0.855263
107 AOC 0.401961 0.833333
108 ACP 0.401869 0.78481
109 HEJ 0.401869 0.782051
110 ATP 0.401869 0.782051
111 LAD 0.401709 0.780488
112 WAQ 0.401709 0.756098
113 YLB 0.401575 0.764706
114 YLC 0.401575 0.783133
115 B4P 0.4 0.805195
116 AP5 0.4 0.805195
117 ACQ 0.4 0.78481
118 4AD 0.4 0.810127
119 YLP 0.4 0.764706
120 NSS 0.4 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4QBK; Ligand: 3NZ; 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: 4qbk.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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