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 = 0.000000064 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 = 0.000000064 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
2 4QBK Kd = 0.000000064 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 = 0.000000064 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
4 4QBK Kd = 0.000000064 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 = 0.000000064 M 5AE C8 H12 N4 O5 C1=NC(=NC(....
4 4QBK Kd = 0.000000064 M 3NZ C20 H25 N7 O5 COc1ccc(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 3NZ; Similar ligands found: 124
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 SO8 0.471154 0.875
11 5X8 0.470588 0.847222
12 NVA 2AD 0.461538 0.890411
13 GLU GMC 0.458716 0.868421
14 LSS 0.45045 0.711111
15 XYA 0.449438 0.884058
16 RAB 0.449438 0.884058
17 ADN 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 SMM 0.440367 0.8
26 SSA 0.440367 0.747126
27 5N5 0.43956 0.857143
28 A 0.438776 0.779221
29 AMP 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 NWW 0.434783 0.797101
37 5CD 0.434783 0.816901
38 FYA 0.434783 0.818182
39 SA8 0.433962 0.828947
40 QA7 0.432432 0.765432
41 53H 0.432432 0.688889
42 TSB 0.432432 0.724138
43 5CA 0.432432 0.747126
44 M2T 0.431579 0.789474
45 NEC 0.43 0.830986
46 9ZD 0.428571 0.777778
47 9ZA 0.428571 0.777778
48 SFG 0.428571 0.833333
49 WSA 0.427419 0.735632
50 S7M 0.427273 0.78481
51 SRP 0.427273 0.820513
52 MTA 0.427083 0.833333
53 5AD 0.426966 0.782609
54 GSU 0.426087 0.707865
55 SAM 0.425926 0.807692
56 45A 0.425743 0.805195
57 ABM 0.425743 0.805195
58 J7C 0.425743 0.802632
59 0UM 0.424779 0.818182
60 AMO 0.424779 0.820513
61 52H 0.423423 0.688889
62 SON 0.423077 0.775
63 7D5 0.42268 0.725
64 NB8 0.422414 0.790123
65 7D7 0.422222 0.777778
66 GJV 0.421569 0.782051
67 7MD 0.421488 0.783133
68 DLL 0.421053 0.794872
69 PAP 0.420561 0.769231
70 AMP MG 0.42 0.789474
71 8LQ 0.419643 0.797468
72 CA0 0.419048 0.78481
73 3DH 0.418367 0.808219
74 NWQ 0.418367 0.826087
75 SAI 0.416667 0.813333
76 DTA 0.416667 0.797297
77 SAH 0.416667 0.824324
78 G5A 0.416667 0.727273
79 8QN 0.415929 0.794872
80 N5O 0.415842 0.873239
81 KG4 0.415094 0.78481
82 8LH 0.414414 0.797468
83 KAA 0.413793 0.703297
84 5AS 0.413462 0.688889
85 ADP 0.413462 0.782051
86 GAP 0.412844 0.78481
87 PAJ 0.412281 0.780488
88 A2D 0.411765 0.805195
89 PRX 0.411215 0.7625
90 ME8 0.410256 0.783133
91 LMS 0.41 0.689655
92 AN2 0.409524 0.772152
93 V2G 0.409091 0.768293
94 PPS 0.409091 0.689655
95 8LE 0.409091 0.765432
96 NVA LMS 0.408696 0.703297
97 XAH 0.408333 0.761905
98 N5A 0.407767 0.84507
99 DAL AMP 0.40708 0.794872
100 KB1 0.40678 0.794872
101 OVE 0.405941 0.75
102 SRA 0.405941 0.740741
103 AU1 0.40566 0.7625
104 M33 0.40566 0.818182
105 LEU LMS 0.405172 0.719101
106 2AM 0.40404 0.779221
107 A12 0.403846 0.775
108 AP2 0.403846 0.775
109 BA3 0.403846 0.805195
110 HZ2 0.403226 0.855263
111 AOC 0.401961 0.833333
112 ACP 0.401869 0.78481
113 HEJ 0.401869 0.782051
114 ATP 0.401869 0.782051
115 WAQ 0.401709 0.756098
116 LAD 0.401709 0.780488
117 YLB 0.401575 0.764706
118 YLC 0.401575 0.783133
119 B4P 0.4 0.805195
120 4AD 0.4 0.810127
121 NSS 0.4 0.727273
122 YLP 0.4 0.764706
123 AP5 0.4 0.805195
124 ACQ 0.4 0.78481
Similar Ligands (3D)
Ligand no: 1; Ligand: 3NZ; Similar ligands found: 0
No: Ligand Similarity coefficient
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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