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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: 111
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 NVA 2AD 0.461538 0.890411
13 LSS 0.45045 0.711111
14 ADN 0.449438 0.884058
15 RAB 0.449438 0.884058
16 XYA 0.449438 0.884058
17 6RE 0.44898 0.792208
18 EEM 0.448598 0.807692
19 FA5 0.448276 0.820513
20 AHX 0.446429 0.8125
21 A3P 0.445545 0.75641
22 A5A 0.444444 0.712644
23 3AM 0.443299 0.766234
24 SSA 0.440367 0.747126
25 SMM 0.440367 0.8
26 5N5 0.43956 0.857143
27 AMP 0.438776 0.779221
28 A 0.438776 0.779221
29 DSZ 0.4375 0.727273
30 54H 0.436364 0.696629
31 VMS 0.436364 0.696629
32 EP4 0.43617 0.810811
33 5AL 0.435185 0.794872
34 A4D 0.434783 0.857143
35 FYA 0.434783 0.818182
36 5CD 0.434783 0.816901
37 SA8 0.433962 0.828947
38 TSB 0.432432 0.724138
39 5CA 0.432432 0.747126
40 53H 0.432432 0.688889
41 M2T 0.431579 0.789474
42 NEC 0.43 0.830986
43 9ZD 0.428571 0.777778
44 SFG 0.428571 0.833333
45 9ZA 0.428571 0.777778
46 WSA 0.427419 0.735632
47 SRP 0.427273 0.820513
48 S7M 0.427273 0.78481
49 MTA 0.427083 0.833333
50 5AD 0.426966 0.782609
51 GSU 0.426087 0.707865
52 SAM 0.425926 0.807692
53 ABM 0.425743 0.805195
54 J7C 0.425743 0.802632
55 0UM 0.424779 0.818182
56 AMO 0.424779 0.820513
57 52H 0.423423 0.688889
58 SON 0.423077 0.775
59 7D5 0.42268 0.725
60 NB8 0.422414 0.790123
61 7D7 0.422222 0.777778
62 GJV 0.421569 0.782051
63 7MD 0.421488 0.783133
64 DLL 0.421053 0.794872
65 PAP 0.420561 0.769231
66 CA0 0.419048 0.78481
67 3DH 0.418367 0.808219
68 DTA 0.416667 0.797297
69 TYR AMP 0.416667 0.833333
70 G5A 0.416667 0.727273
71 SAH 0.416667 0.824324
72 SAI 0.416667 0.813333
73 8QN 0.415929 0.794872
74 KAA 0.413793 0.703297
75 5AS 0.413462 0.688889
76 ADP 0.413462 0.782051
77 GAP 0.412844 0.78481
78 PAJ 0.412281 0.780488
79 A2D 0.411765 0.805195
80 PRX 0.411215 0.7625
81 ME8 0.410256 0.783133
82 LMS 0.41 0.689655
83 AN2 0.409524 0.772152
84 PPS 0.409091 0.689655
85 NVA LMS 0.408696 0.703297
86 XAH 0.408333 0.761905
87 DAL AMP 0.40708 0.794872
88 KB1 0.40678 0.794872
89 SRA 0.405941 0.740741
90 OVE 0.405941 0.75
91 M33 0.40566 0.818182
92 AU1 0.40566 0.7625
93 LEU LMS 0.405172 0.703297
94 2AM 0.40404 0.779221
95 A12 0.403846 0.775
96 BA3 0.403846 0.805195
97 AP2 0.403846 0.775
98 AOC 0.401961 0.833333
99 ACP 0.401869 0.78481
100 ATP 0.401869 0.782051
101 HEJ 0.401869 0.782051
102 WAQ 0.401709 0.756098
103 LAD 0.401709 0.780488
104 YLC 0.401575 0.783133
105 YLB 0.401575 0.764706
106 NSS 0.4 0.727273
107 ACQ 0.4 0.78481
108 YLP 0.4 0.764706
109 AP5 0.4 0.805195
110 4AD 0.4 0.810127
111 B4P 0.4 0.805195
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: 135
This union binding pocket(no: 1) in the query (biounit: 4qbk.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 4WG0 CHD None
3 2HMT NAI None
4 1GSA ADP None
5 5RHN 8BR None
6 3CH6 311 1.03093
7 3CH6 NAP 1.03093
8 1GNI OLA 1.54639
9 5ZM0 FAD 2.06186
10 2ART LPA AMP 2.06186
11 5LNE A2G GAL 2.43902
12 6CGN DA 2.57732
13 3EWC MCF 2.57732
14 2A3I C0R 2.57732
15 5N5U 7N8 2.57732
16 3FHR P4O 2.57732
17 1OAA OAA 2.57732
18 5CX6 CDP 2.57732
19 5UGW GSH 2.85714
20 1J6W MET 2.85714
21 4PLT NAI 3.09278
22 4PLT OXM 3.09278
23 3AQT RCO 3.09278
24 2Q2Y MKR 3.09278
25 2Q2Y ADP 3.09278
26 4G2R H1L 3.09278
27 3FYS PLM 3.09278
28 6GL8 F3Q 3.48837
29 2ZJ1 ARJ 3.60825
30 2ZJ1 NAD 3.60825
31 1N46 PFA 3.60825
32 2UYQ SAM 3.60825
33 3MDV CL6 3.60825
34 1OPK MYR 3.60825
35 1GZ4 ATP 3.60825
36 4GJ3 0XP 3.60825
37 1X7D NAD 3.60825
38 1YKI NFZ 3.68664
39 3RET SAL 3.9604
40 3RET PYR 3.9604
41 3KO0 TFP 3.9604
42 5ECP JAA 4.12371
43 5ECP MET 4.12371
44 5ECP ATP 4.12371
45 6ALW BMJ 4.12371
46 6ALW BNV 4.12371
47 2GU8 796 4.12371
48 4A0S NAP 4.12371
49 4ZY1 4U5 4.12371
50 5OSW DIU 4.12371
51 1EP2 ORO 4.12371
52 3OID NDP 4.12371
53 3MQG ACO 4.16667
54 2RGO FAD 4.61285
55 4DPL NAP 4.63918
56 1W3R PYR 4.63918
57 3FPZ AHZ 4.63918
58 1COY FAD 4.63918
59 2IVN ANP 4.63918
60 4Y1B NAP 5.15464
61 1MGP PLM 5.15464
62 1VPV PLM 5.15464
63 6ADI 9UO 5.15464
64 4J4H NAI 5.15464
65 4J4H 1J1 5.15464
66 5LX9 OLB 5.15464
67 2B3D FAD 5.15464
68 4JK3 NAD 5.15464
69 1YQD NAP 5.15464
70 4GUT FAD 5.64516
71 4B7X NAP 5.6701
72 5H1W LER 5.6701
73 3WYJ H78 5.6701
74 1E5D FMN 5.6701
75 6FTB M0E 5.6701
76 1NVM NAD 6.08974
77 4K26 SFF 6.18557
78 1R55 097 6.18557
79 3JZB 4HY 6.70103
80 6A56 LAT 6.70732
81 3G4G D71 7.2165
82 2A92 NAI 7.2165
83 5YU3 NAD 7.2165
84 5YU3 PRO 7.2165
85 5N7O 69Y 7.23982
86 5KKA 6V0 7.37179
87 3AYI HCI 7.73196
88 3AYI FAD 7.73196
89 5O2N FLC 7.73196
90 3BQD DAY 7.73196
91 5G5W R8C 7.73196
92 1V8B NAD 7.73196
93 1QM5 PLP 7.73196
94 1QM5 GLC GLC GLC PO4 SGC GLC 7.73196
95 4P6X HCY 7.73196
96 5C9J DAO 8.24742
97 3B9Z CO2 8.24742
98 2DC1 CIT 8.24742
99 2C6Q NDP 8.24742
100 3HB5 E2B 8.24742
101 3TTI KBI 8.24742
102 5C9J STE 8.24742
103 2XBK XBK 8.41584
104 4M52 M52 8.76289
105 6F3M NAD 9.27835
106 3KXC PLM 9.79381
107 5FOI MY8 9.79381
108 1PZX PLM 9.79381
109 5AX9 4KT 9.79381
110 2Z9I GLY ALA THR VAL 10.3093
111 5JZJ AN2 10.3093
112 5X9D 80F 10.8247
113 1VL8 NAP 10.8247
114 5K2M ADP 10.8247
115 5LXT GTP 11.8557
116 1QNF FAD 11.8557
117 1SR7 MOF 12.3711
118 2PHF MAN MAN BMA MAN 12.6984
119 2PHX MAN MAN MAN MAN 12.6984
120 2PHR MAN MAN BMA MAN 12.6984
121 1Q8V MAN MAN MAN 12.6984
122 2AR6 NAG MAN MAN MAN NAG 12.6984
123 5Z84 CHD 14.433
124 2Y69 CHD 14.433
125 5ZCO CHD 14.433
126 5W97 CHD 14.433
127 1E8G FCR 15.4639
128 4WGF HX2 16.4948
129 5C1M OLC 16.4948
130 3H0A D30 17.5258
131 5NNT DPV 18.9189
132 1EZV SMA 18.9189
133 4HSU FAD 20
134 3AD8 NAD 25.2525
135 4GUS FAD 28.5714
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