Receptor
PDB id Resolution Class Description Source Keywords
3URB 1.77 Å EC: 3.1.8.1 CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/ BREVUNDIMONAS DIMINUTA METALLOENZYME TIM BARREL NERVE AGENTS PHOSPHOTRIESTERASEHYDROLASE
Ref.: ENZYMES FOR THE HOMELAND DEFENSE: OPTIMIZING PHOSPHOTRIESTERASE FOR THE HYDROLYSIS OF ORGANOPHOS NERVE AGENTS. BIOCHEMISTRY V. 51 6463 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:801;
A:802;
B:803;
B:804;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
58.933 Co [Co+2...
DPF A:903;
B:902;
 Valid;
Valid;
 none;
none;
 submit data
154.102 C4 H11 O4 P CCOP(...
IMD A:901;
 Invalid;
 none;
 submit data
69.085 C3 H5 N2 c1c[n...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3URB 1.77 Å EC: 3.1.8.1 CRYSTAL STRUCTURE OF PTE MUTANT H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/ BREVUNDIMONAS DIMINUTA METALLOENZYME TIM BARREL NERVE AGENTS PHOSPHOTRIESTERASEHYDROLASE
Ref.: ENZYMES FOR THE HOMELAND DEFENSE: OPTIMIZING PHOSPHOTRIESTERASE FOR THE HYDROLYSIS OF ORGANOPHOS NERVE AGENTS. BIOCHEMISTRY V. 51 6463 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3URB - DPF C4 H11 O4 P CCOP(=O)(O....
2 3URN - QMP C7 H15 O3 P CP(=O)(O)O....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2R1K - DPF C4 H11 O4 P CCOP(=O)(O....
2 1EZ2 - DII C7 H17 O3 P CC(C)OP(=O....
3 1JGM - PEL C8 H10 O c1ccc(cc1)....
4 2D2H - TZZ C3 H9 O4 P COP(=O)(OC....
5 3C86 - DPJ C4 H11 O3 P S CCOP(=S)(O....
6 1EYW - TEN C6 H15 O4 P CCOP(=O)(O....
7 3OOD - EPL C11 H17 O5 P CCOP(=O)(O....
8 3E3H - EBP C12 H19 O3 P CCOP(=O)(C....
9 3URQ - QMP C7 H15 O3 P CP(=O)(O)O....
10 3A3W - EPL C11 H17 O5 P CCOP(=O)(O....
11 1I0B - PEL C8 H10 O c1ccc(cc1)....
12 1HZY - PEL C8 H10 O c1ccc(cc1)....
13 3CAK - DPF C4 H11 O4 P CCOP(=O)(O....
14 1DPM - EBP C12 H19 O3 P CCOP(=O)(C....
15 2R1P - DPJ C4 H11 O3 P S CCOP(=S)(O....
16 1P6C - EBP C12 H19 O3 P CCOP(=O)(C....
17 1I0D - PEL C8 H10 O c1ccc(cc1)....
18 3UR5 - DPF C4 H11 O4 P CCOP(=O)(O....
19 2R1M - DPF C4 H11 O4 P CCOP(=O)(O....
20 2D2G - DZZ C2 H7 O3 P S COP(=S)(O)....
21 1QW7 - EBP C12 H19 O3 P CCOP(=O)(C....
22 2R1N - EPL C11 H17 O5 P CCOP(=O)(O....
23 2R1L - DPJ C4 H11 O3 P S CCOP(=S)(O....
24 4NP7 - DPJ C4 H11 O3 P S CCOP(=S)(O....
25 1PSC - EBP C12 H19 O3 P CCOP(=O)(C....
26 1P6B - EFS C2 H7 O4 P CCOP(=O)(O....
27 3URB - DPF C4 H11 O4 P CCOP(=O)(O....
28 3URN - QMP C7 H15 O3 P CP(=O)(O)O....
29 4E3T - HLN C16 H21 O3 P CCCCCCP(=O....
50% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2R1K - DPF C4 H11 O4 P CCOP(=O)(O....
2 1EZ2 - DII C7 H17 O3 P CC(C)OP(=O....
3 1JGM - PEL C8 H10 O c1ccc(cc1)....
4 2D2H - TZZ C3 H9 O4 P COP(=O)(OC....
5 3C86 - DPJ C4 H11 O3 P S CCOP(=S)(O....
6 1EYW - TEN C6 H15 O4 P CCOP(=O)(O....
7 3OOD - EPL C11 H17 O5 P CCOP(=O)(O....
8 3E3H - EBP C12 H19 O3 P CCOP(=O)(C....
9 3URQ - QMP C7 H15 O3 P CP(=O)(O)O....
10 3A3W - EPL C11 H17 O5 P CCOP(=O)(O....
11 1I0B - PEL C8 H10 O c1ccc(cc1)....
12 1HZY - PEL C8 H10 O c1ccc(cc1)....
13 3CAK - DPF C4 H11 O4 P CCOP(=O)(O....
14 1DPM - EBP C12 H19 O3 P CCOP(=O)(C....
15 2R1P - DPJ C4 H11 O3 P S CCOP(=S)(O....
16 1P6C - EBP C12 H19 O3 P CCOP(=O)(C....
17 1I0D - PEL C8 H10 O c1ccc(cc1)....
18 3UR5 - DPF C4 H11 O4 P CCOP(=O)(O....
19 2R1M - DPF C4 H11 O4 P CCOP(=O)(O....
20 2D2G - DZZ C2 H7 O3 P S COP(=S)(O)....
21 1QW7 - EBP C12 H19 O3 P CCOP(=O)(C....
22 2R1N - EPL C11 H17 O5 P CCOP(=O)(O....
23 2R1L - DPJ C4 H11 O3 P S CCOP(=S)(O....
24 4NP7 - DPJ C4 H11 O3 P S CCOP(=S)(O....
25 1PSC - EBP C12 H19 O3 P CCOP(=O)(C....
26 1P6B - EFS C2 H7 O4 P CCOP(=O)(O....
27 3URB - DPF C4 H11 O4 P CCOP(=O)(O....
28 3URN - QMP C7 H15 O3 P CP(=O)(O)O....
29 4RDZ - MYR C14 H28 O2 CCCCCCCCCC....
30 4E3T - HLN C16 H21 O3 P CCCCCCP(=O....
31 4H9X - HL4 C8 H13 N O3 CCCC(=O)N[....
32 6JST - LAE C12 H19 N O4 CCCCCC(=O)....
33 4H9T - HL4 C8 H13 N O3 CCCC(=O)N[....
34 4KF1 - HT5 C14 H25 N O2 S CCCCCCCCCC....
35 2VC7 Ki = 432.7 uM HT5 C14 H25 N O2 S CCCCCCCCCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DPF; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 DPF 1 1
2 EFS 0.6 0.821429
3 VX 0.571429 0.857143
4 P22 0.56 0.741935
5 TEN 0.454545 0.884615
6 DPJ 0.416667 0.866667
Similar Ligands (3D)
Ligand no: 1; Ligand: DPF; Similar ligands found: 297
No: Ligand Similarity coefficient
1 MEV 0.9554
2 1CO 0.9386
3 HSE 0.9367
4 98J 0.9344
5 AUD 0.9313
6 ORN 0.9293
7 MAH 0.9269
8 VPR 0.9233
9 TAR 0.9225
10 ASN 0.9219
11 4SD 0.9215
12 2DR 0.9203
13 ICN 0.9193
14 TLA 0.9186
15 XYL 0.9177
16 RB5 0.9177
17 RB0 0.9177
18 MLT 0.9174
19 QFH 0.9174
20 LEU 0.9169
21 MRY 0.9155
22 23B 0.9143
23 NVA 0.9141
24 PG0 0.9131
25 OAA 0.9130
26 DII 0.9129
27 TZZ 0.9124
28 DIG 0.9121
29 OEM 0.9120
30 ILE 0.9119
31 ROR 0.9111
32 DAS 0.9102
33 XLS 0.9100
34 IXW 0.9080
35 QDK 0.9080
36 HDA 0.9076
37 MET 0.9074
38 AHB 0.9063
39 HCS 0.9056
40 TEO 0.9055
41 DZZ 0.9054
42 1SP 0.9051
43 2AS 0.9050
44 NXA 0.9042
45 FW5 0.9035
46 RBL 0.9030
47 M44 0.9027
48 WTZ 0.9026
49 LMR 0.9025
50 HTX 0.9021
51 IOM 0.9020
52 8EW 0.9017
53 DMV 0.9017
54 DCL 0.9014
55 ASP 0.9013
56 8EZ 0.9011
57 5ZE 0.9011
58 EHM 0.9009
59 9X7 0.9009
60 CRN 0.9006
61 HYA 0.8995
62 SIN 0.8993
63 KMT 0.8992
64 MD0 0.8986
65 P4B 0.8984
66 5FX 0.8982
67 MED 0.8979
68 XUL 0.8976
69 MSE 0.8972
70 HZP 0.8969
71 DTL 0.8968
72 CMS 0.8968
73 2CO 0.8962
74 SRT 0.8958
75 UY7 0.8958
76 NFQ 0.8956
77 5AN 0.8955
78 6JN 0.8955
79 ERH 0.8951
80 GLU 0.8951
81 6UA 0.8949
82 BR8 0.8944
83 DGL 0.8943
84 THE 0.8943
85 9YL 0.8941
86 CYS 0.8939
87 13X 0.8934
88 6NA 0.8933
89 VAL 0.8933
90 TMH 0.8933
91 LER 0.8932
92 AKG 0.8929
93 TCZ 0.8929
94 DTU 0.8925
95 AX2 0.8924
96 PBE 0.8924
97 SGL 0.8923
98 9J3 0.8923
99 THR 0.8917
100 MLE 0.8916
101 DGY 0.8916
102 KMH 0.8913
103 WDL 0.8913
104 NLE 0.8911
105 ITN 0.8909
106 2FT 0.8908
107 CIZ 0.8903
108 2RH 0.8896
109 69O 0.8895
110 3AY 0.8893
111 AC5 0.8893
112 PAF 0.8884
113 PCA 0.8883
114 16D 0.8880
115 AH8 0.8878
116 X1R 0.8878
117 GUA 0.8878
118 MPJ 0.8877
119 2EH 0.8876
120 2ZX 0.8875
121 MZW 0.8870
122 LNO 0.8869
123 7UC 0.8861
124 DTT 0.8858
125 SC2 0.8847
126 Q07 0.8846
127 VKC 0.8843
128 PG3 0.8841
129 AKB 0.8841
130 IHG 0.8836
131 VAH 0.8836
132 YIV 0.8836
133 COI 0.8832
134 OCT 0.8829
135 NK 0.8827
136 CRS 0.8826
137 2KT 0.8821
138 OHG 0.8821
139 UGC 0.8820
140 H76 0.8820
141 R8A 0.8819
142 ACA 0.8817
143 R1X 0.8817
144 2RA 0.8816
145 RCO 0.8815
146 8GL 0.8813
147 ALO 0.8811
148 MAE 0.8809
149 AG2 0.8808
150 AHR 0.8808
151 BP9 0.8802
152 PAE 0.8801
153 32O 0.8800
154 PEP 0.8800
155 2HG 0.8799
156 LG5 0.8797
157 CXF 0.8792
158 COM 0.8792
159 NLP 0.8791
160 HYP 0.8788
161 0CG 0.8785
162 MUC 0.8785
163 SSN 0.8784
164 LG3 0.8783
165 FPK 0.8783
166 23W 0.8782
167 SNE 0.8778
168 N6C 0.8774
169 3HG 0.8774
170 RNS 0.8773
171 S76 0.8772
172 URP 0.8772
173 9TY 0.8771
174 TIU 0.8771
175 7WG 0.8767
176 TZE 0.8765
177 URA 0.8764
178 R2B 0.8761
179 DSN 0.8760
180 TZL 0.8760
181 2PG 0.8759
182 PPR 0.8759
183 7A8 0.8758
184 4H2 0.8756
185 2IT 0.8755
186 HBA 0.8755
187 5HY 0.8752
188 M3T 0.8751
189 CDV 0.8750
190 3SY 0.8750
191 8X3 0.8750
192 LDU 0.8748
193 N8P 0.8743
194 RUU 0.8740
195 CIG 0.8739
196 911 0.8736
197 IMR 0.8735
198 284 0.8734
199 URQ 0.8734
200 3CH 0.8732
201 B3R 0.8732
202 HGQ 0.8731
203 26D 0.8731
204 SD4 0.8731
205 40E 0.8729
206 280 0.8728
207 TFB 0.8727
208 OGA 0.8726
209 3GR 0.8726
210 FP1 0.8726
211 CSS 0.8722
212 FQI 0.8720
213 2A7 0.8719
214 RIB 0.8719
215 OPE 0.8712
216 DGN 0.8710
217 HY3 0.8710
218 FOC 0.8709
219 CHT 0.8709
220 I2M 0.8707
221 CIT 0.8704
222 LYS 0.8701
223 2HE 0.8698
224 261 0.8698
225 7C3 0.8695
226 AL0 0.8694
227 ONL 0.8693
228 A3B 0.8693
229 RNT 0.8692
230 GLY CYS 0.8691
231 AE3 0.8685
232 CP 0.8684
233 IDH 0.8679
234 P7I 0.8678
235 PGA 0.8673
236 GXV 0.8671
237 DCY 0.8670
238 FLC 0.8670
239 1P3 0.8669
240 12M 0.8668
241 ETM 0.8667
242 GGL 0.8667
243 ZBT 0.8665
244 GLY GLY 0.8664
245 XPO 0.8662
246 DMJ 0.8656
247 5AC 0.8656
248 PSJ 0.8654
249 CNL 0.8654
250 IQ0 0.8652
251 192 0.8651
252 CUW 0.8650
253 FAN 0.8647
254 ABU 0.8642
255 TAU 0.8640
256 Z6J 0.8637
257 PRO 0.8633
258 LEA 0.8633
259 ZZ3 0.8632
260 DLY 0.8621
261 3Z7 0.8619
262 II6 0.8619
263 M2H 0.8619
264 C2A 0.8618
265 TB6 0.8614
266 SMB 0.8612
267 YCP 0.8609
268 IFL 0.8608
269 60P 0.8607
270 5XB 0.8603
271 SOR 0.8602
272 CAM 0.8599
273 S2G 0.8597
274 ASF 0.8595
275 BSX 0.8594
276 AMC 0.8592
277 285 0.8591
278 HPY 0.8583
279 K6V 0.8582
280 TRC 0.8580
281 266 0.8579
282 GIF 0.8572
283 JZ1 0.8566
284 FBJ 0.8565
285 FJO 0.8563
286 1KA 0.8563
287 POA 0.8563
288 GBN 0.8563
289 3SL 0.8562
290 0OC 0.8560
291 KPL 0.8557
292 9SB 0.8555
293 AOS 0.8552
294 DGJ 0.8550
295 34V 0.8544
296 IP0 0.8527
297 O7U 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3URB; Ligand: DPF; 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: 3urb.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3URB; Ligand: DPF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3urb.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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