Receptor
PDB id Resolution Class Description Source Keywords
4QD3 1.89 Å EC: 3.1.1.29 CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM PSEUDOMONA AERUGINOSA WITH 5-AZACYTIDINE AT 1.89 ANGSTROM RESOLUTION PSEUDOMONAS AERUGINOSA 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
5AE A:201;
Valid;
none;
Kd = 0.000000064 M
244.205 C8 H12 N4 O5 C1=NC...
GOL A:202;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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: 5AE; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 5AE 1 1
2 CTN 0.542373 0.935484
3 AR3 0.542373 0.935484
4 F01 0.52459 0.865672
5 CTD 0.483333 0.854839
6 ZEB 0.419355 0.887097
7 URD 0.412698 0.777778
8 URI 0.412698 0.887097
9 DHZ 0.40625 0.887097
10 DKZ 0.405797 0.80597
11 5HM 0.405405 0.794521
12 5UD 0.4 0.820895
13 2TU 0.4 0.818182
14 BRD 0.4 0.83871
Similar Ligands (3D)
Ligand no: 1; Ligand: 5AE; Similar ligands found: 235
No: Ligand Similarity coefficient
1 DCZ 0.9766
2 DUR 0.9705
3 GEO 0.9572
4 TYU 0.9563
5 I5A 0.9543
6 THM 0.9530
7 UUA 0.9522
8 THU 0.9493
9 0DN 0.9474
10 MCY 0.9426
11 DDU 0.9419
12 5BT 0.9393
13 ID2 0.9382
14 K80 0.9379
15 ADN 0.9297
16 B86 0.9283
17 PIR 0.9267
18 SCT 0.9267
19 1KN 0.9213
20 NOS 0.9187
21 A 0.9184
22 HPR 0.9171
23 PRH 0.9171
24 1DA 0.9166
25 3D1 0.9165
26 5MD 0.9159
27 TBN 0.9157
28 TMC 0.9154
29 B2T 0.9138
30 Z15 0.9136
31 9DI 0.9131
32 5N5 0.9125
33 FMB 0.9124
34 AHU 0.9123
35 PUR 0.9117
36 W29 0.9115
37 UA2 0.9109
38 X11 0.9096
39 FC2 0.9075
40 PQT 0.9072
41 IMH 0.9063
42 5AD 0.9059
43 5CD 0.9053
44 TIZ 0.9052
45 RBV 0.9048
46 2GD 0.9042
47 FMC 0.9031
48 6MD 0.9031
49 3DT 0.9028
50 HNL 0.9021
51 XYA 0.9013
52 5ID 0.9000
53 MZR 0.8984
54 5NB 0.8976
55 WVV 0.8967
56 16Z 0.8965
57 BP3 0.8961
58 WOE 0.8955
59 DNB 0.8947
60 5JT 0.8946
61 M02 0.8945
62 EKH 0.8936
63 EAT 0.8935
64 FTU 0.8935
65 TI7 0.8932
66 U 0.8930
67 6HX 0.8930
68 1FL 0.8929
69 OA1 0.8929
70 5FD 0.8920
71 6J3 0.8919
72 B4O 0.8914
73 MTA 0.8911
74 MTP 0.8903
75 XDK 0.8899
76 IQQ 0.8898
77 3BH 0.8896
78 DBM 0.8893
79 A4D 0.8892
80 L13 0.8891
81 AD3 0.8889
82 TIA 0.8883
83 TRP 0.8882
84 X6P 0.8881
85 BPY 0.8880
86 RFZ 0.8873
87 M3E 0.8870
88 R9G 0.8869
89 FHI 0.8868
90 A6H 0.8865
91 FCD 0.8864
92 AUV 0.8860
93 PF1 0.8859
94 ZIQ 0.8850
95 ZYV 0.8848
96 GMP 0.8844
97 L5D 0.8844
98 FTV 0.8844
99 9W5 0.8842
100 EAJ 0.8840
101 H70 0.8829
102 HNH 0.8829
103 KTJ 0.8825
104 MUK 0.8825
105 EXR 0.8824
106 3IL 0.8820
107 7ZL 0.8819
108 U5P 0.8814
109 ENG 0.8813
110 XYP XIF 0.8813
111 XIF XYP 0.8813
112 1ER 0.8806
113 50C 0.8802
114 WL3 0.8799
115 HNK 0.8799
116 7D7 0.8797
117 HVE 0.8797
118 NNR 0.8791
119 43F 0.8789
120 977 0.8789
121 JO8 0.8783
122 38B 0.8781
123 QBS 0.8781
124 TT4 0.8780
125 1A7 0.8773
126 ID8 0.8772
127 P2L 0.8771
128 AZZ 0.8770
129 F63 0.8769
130 0FR 0.8768
131 6J9 0.8768
132 9FH 0.8765
133 KYN 0.8765
134 S1D 0.8759
135 4OG 0.8755
136 N2Y 0.8753
137 X48 0.8750
138 OX2 0.8749
139 B21 0.8747
140 GNG 0.8742
141 9UL 0.8740
142 PBQ 0.8739
143 1Z6 0.8735
144 F16 0.8733
145 5F8 0.8725
146 78U 0.8723
147 DTR 0.8723
148 61M 0.8719
149 FB4 0.8713
150 JF8 0.8710
151 BP6 0.8706
152 GNW 0.8700
153 QTS 0.8699
154 VBC 0.8693
155 DIF 0.8691
156 27M 0.8690
157 NCT 0.8686
158 TCL 0.8685
159 FMQ 0.8684
160 AVA 0.8683
161 C0H 0.8683
162 MIL 0.8683
163 CC5 0.8680
164 XDL XYP 0.8680
165 IMK 0.8680
166 A4T 0.8679
167 CL9 0.8677
168 C5P 0.8677
169 U2Z 0.8672
170 26C 0.8667
171 BQ5 0.8667
172 I2E 0.8664
173 8OE 0.8663
174 8UY 0.8658
175 S2T 0.8657
176 QUS 0.8656
177 DTY 0.8655
178 8CB 0.8650
179 4I8 0.8649
180 MXD 0.8643
181 RUG 0.8641
182 89J 0.8639
183 2JM 0.8634
184 B2Y 0.8634
185 EZN 0.8633
186 5E4 0.8630
187 54E 0.8627
188 RQD 0.8627
189 Y4L 0.8627
190 MPK 0.8627
191 YOF 0.8626
192 JRB 0.8625
193 A4G 0.8623
194 JSX 0.8622
195 79W 0.8621
196 92G 0.8620
197 9FG 0.8620
198 Q4G 0.8620
199 3Y7 0.8618
200 5P3 0.8617
201 KP2 0.8616
202 EXL 0.8615
203 ISC 0.8614
204 DTE 0.8614
205 BRH 0.8612
206 LTN 0.8611
207 HWD 0.8609
208 3B4 0.8608
209 CH9 0.8606
210 CFE 0.8601
211 HVJ 0.8601
212 VXX 0.8600
213 26A 0.8599
214 FWD 0.8598
215 PFF 0.8596
216 4EU 0.8592
217 TQL 0.8587
218 A4V 0.8585
219 FT2 0.8584
220 U4J 0.8579
221 C2M 0.8577
222 22L 0.8576
223 YF3 0.8574
224 IYR 0.8573
225 B23 0.8570
226 5I5 0.8567
227 CUT 0.8565
228 DAH 0.8563
229 AWE 0.8559
230 G14 0.8547
231 51Y 0.8541
232 2J5 0.8541
233 FC3 0.8533
234 FUZ 0.8526
235 HO4 0.8525
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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