Receptor
PDB id Resolution Class Description Source Keywords
5GZ6 1.74 Å EC: 1.4.1.16 STRUCTURE OF D-AMINO ACID DEHYDROGENASE IN COMPLEX WITH NADP KETO-6-AMINOCAPRONIC ACID UREIBACILLUS THERMOSPHAERICUS ROSSMANN FOLD OXIDOREDUCTASE
Ref.: STRUCTURE-BASED ENGINEERING OF AN ARTIFICIALLY GENE NADP+-DEPENDENT D-AMINO ACID DEHYDROGENASE APPL. ENVIRON. MICROBIOL. V. 83 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:3002;
A:1003;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
NDP A:1001;
Valid;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
7C3 A:1002;
Valid;
none;
submit data
145.156 C6 H11 N O3 C(CCN...
ACT B:3001;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GZ6 1.74 Å EC: 1.4.1.16 STRUCTURE OF D-AMINO ACID DEHYDROGENASE IN COMPLEX WITH NADP KETO-6-AMINOCAPRONIC ACID UREIBACILLUS THERMOSPHAERICUS ROSSMANN FOLD OXIDOREDUCTASE
Ref.: STRUCTURE-BASED ENGINEERING OF AN ARTIFICIALLY GENE NADP+-DEPENDENT D-AMINO ACID DEHYDROGENASE APPL. ENVIRON. MICROBIOL. V. 83 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5GZ3 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 3WYC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 5GZ6 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5GZ3 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 3WYC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 5GZ6 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5GZ3 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 3WYC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 5GZ6 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 1F06 Ki = 5 uM 2NP C8 H13 N O4 C=C(CCC[C@....
5 1DAP - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
6 3DAP - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
7 2DAP - API C7 H14 N2 O4 C(C[C@H](C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NDP; Similar ligands found: 180
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 NDP DTT 0.528169 0.891566
25 6V0 0.519685 0.974026
26 NAP 0.514493 0.922078
27 7L1 0.507143 0.763441
28 EAD 0.507143 0.949367
29 A2D 0.504673 0.921053
30 TXE 0.503876 0.935897
31 NA0 0.496454 0.910256
32 TXD 0.496124 0.911392
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 HQG 0.483051 0.909091
38 PAP 0.482456 0.907895
39 BA3 0.481818 0.921053
40 NAJ PZO 0.478261 0.924051
41 ATP 0.477876 0.921053
42 HEJ 0.477876 0.921053
43 B4P 0.477477 0.921053
44 AP5 0.477477 0.921053
45 ADP 0.477477 0.921053
46 OAD 0.47541 0.897436
47 5FA 0.473684 0.921053
48 APR 0.473684 0.896104
49 AR6 0.473684 0.896104
50 AQP 0.473684 0.921053
51 AN2 0.473214 0.909091
52 3OD 0.467742 0.897436
53 50T 0.464912 0.884615
54 NAJ PYZ 0.464789 0.879518
55 9X8 0.463415 0.851852
56 PO4 PO4 A A A A PO4 0.463415 0.857143
57 V3L 0.461538 0.896104
58 2A5 0.46087 0.85
59 AT4 0.460177 0.886076
60 ADQ 0.459016 0.897436
61 4AD 0.459016 0.875
62 A1R 0.459016 0.841463
63 OVE 0.458716 0.8375
64 OMR 0.458647 0.813953
65 PPS 0.457627 0.811765
66 AD9 0.456897 0.897436
67 CA0 0.45614 0.897436
68 M33 0.45614 0.884615
69 ADJ 0.455882 0.879518
70 A3P 0.455357 0.894737
71 KG4 0.452174 0.897436
72 ACP 0.452174 0.897436
73 ENP 0.451613 0.85
74 UP5 0.451128 0.948052
75 SRP 0.45 0.8625
76 ACQ 0.449153 0.897436
77 ANP 0.449153 0.897436
78 PRX 0.448276 0.82716
79 A3R 0.447154 0.841463
80 5AL 0.445378 0.884615
81 KMQ 0.445312 0.886076
82 7D4 0.443478 0.8375
83 ADX 0.443478 0.811765
84 8LQ 0.442623 0.8625
85 8LH 0.438017 0.8625
86 6YZ 0.438017 0.897436
87 A 0.436364 0.894737
88 AMP 0.436364 0.894737
89 4TC 0.433824 0.924051
90 7D3 0.433628 0.8375
91 DCA 0.433566 0.788889
92 ETB 0.433566 0.797753
93 8LE 0.433333 0.851852
94 1ZZ 0.433071 0.802326
95 BIS 0.433071 0.864198
96 JNT 0.432 0.873418
97 00A 0.432 0.864198
98 QA7 0.430894 0.851852
99 ATF 0.429752 0.886076
100 DQV 0.428571 0.934211
101 0T1 0.427586 0.788889
102 8QN 0.427419 0.884615
103 5SV 0.427419 0.788235
104 3AM 0.427273 0.857143
105 N01 0.426573 0.884615
106 LAD 0.425197 0.821429
107 WAQ 0.425197 0.841463
108 PR8 0.425197 0.811765
109 DTP 0.425 0.8375
110 PAJ 0.424 0.843373
111 AMO 0.424 0.886076
112 APC 0.423729 0.886076
113 UPA 0.423358 0.935897
114 48N 0.422222 0.853659
115 PTJ 0.421875 0.853659
116 FYA 0.421875 0.860759
117 CNA 0.421429 0.910256
118 PUA 0.42069 0.9125
119 DND 0.419118 0.910256
120 AV2 0.418033 0.848101
121 COA 0.417808 0.788889
122 3UK 0.417323 0.897436
123 OOB 0.416 0.909091
124 IVC 0.415584 0.78022
125 DAT 0.415254 0.8375
126 NDO 0.414966 0.897436
127 139 0.414286 0.901235
128 B5V 0.414062 0.886076
129 TAT 0.413223 0.886076
130 3AT 0.413223 0.896104
131 T99 0.413223 0.886076
132 L3W 0.413043 0.960526
133 YLB 0.413043 0.784091
134 62F 0.4125 0.823529
135 45A 0.412281 0.848101
136 ABM 0.412281 0.848101
137 B5M 0.412214 0.875
138 YLP 0.411765 0.784091
139 ME8 0.410853 0.802326
140 NB8 0.410853 0.853659
141 SON 0.410256 0.886076
142 DLL 0.409449 0.909091
143 AHX 0.409449 0.853659
144 COS 0.409396 0.771739
145 AMX 0.409396 0.797753
146 CAO 0.409396 0.763441
147 30N 0.409396 0.72449
148 7D5 0.409091 0.8125
149 4UW 0.408759 0.9125
150 F2R 0.408451 0.825581
151 APX 0.407692 0.841463
152 AMP MG 0.40708 0.857143
153 SRA 0.40708 0.85
154 SCO 0.406667 0.788889
155 CMX 0.406667 0.788889
156 TYM 0.405797 0.886076
157 COD 0.405594 0.777778
158 OXK 0.405229 0.771739
159 CA6 0.405229 0.70297
160 AP2 0.405172 0.886076
161 A12 0.405172 0.886076
162 OZV 0.404762 0.896104
163 9SN 0.40458 0.853659
164 LAQ 0.404412 0.802326
165 T5A 0.404255 0.914634
166 FCX 0.403974 0.763441
167 FAM 0.403974 0.771739
168 ACO 0.403974 0.763441
169 CUU 0.403361 0.896104
170 YLC 0.402878 0.823529
171 1VU 0.402597 0.763441
172 B5Y 0.401515 0.875
173 FA5 0.401515 0.886076
174 HAX 0.401316 0.771739
175 CAJ 0.4 0.771739
176 AR6 AR6 0.4 0.871795
177 TXA 0.4 0.886076
178 APU 0.4 0.923077
179 4UU 0.4 0.948052
180 AFH 0.4 0.843373
Ligand no: 2; Ligand: 7C3; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 7C3 1 1
2 OOG 0.466667 0.642857
3 ACA 0.451613 0.821429
4 011 0.4375 0.793103
5 ABU 0.428571 0.814815
6 8AC 0.424242 0.793103
7 26P 0.416667 0.71875
8 JX7 0.405405 0.722222
Similar Ligands (3D)
Ligand no: 1; Ligand: NDP; Similar ligands found: 6
No: Ligand Similarity coefficient
1 NAD 0.9403
2 NHD 0.9199
3 NAJ 0.9080
4 A3D 0.9036
5 8ID 0.8925
6 NAE 0.8727
Ligand no: 2; Ligand: 7C3; Similar ligands found: 400
No: Ligand Similarity coefficient
1 ONH 0.9819
2 AG2 0.9747
3 LYS 0.9697
4 DLY 0.9673
5 AKG 0.9643
6 KMT 0.9633
7 GLU 0.9609
8 BNF 0.9575
9 MLZ 0.9572
10 MET 0.9555
11 2IT 0.9541
12 OGA 0.9522
13 N6C 0.9520
14 5XA 0.9512
15 NYL 0.9512
16 7OD 0.9494
17 3OM 0.9494
18 GGL 0.9486
19 2HG 0.9479
20 ORN 0.9472
21 CUW 0.9471
22 KQY 0.9437
23 GOJ 0.9425
24 MXN 0.9422
25 3OL 0.9418
26 S2G 0.9412
27 DGL 0.9409
28 3H2 0.9409
29 PRA 0.9408
30 MED 0.9400
31 N4B 0.9381
32 11C 0.9380
33 MHN 0.9377
34 DIR 0.9370
35 GLN 0.9365
36 URO 0.9360
37 OCA 0.9349
38 HPN 0.9333
39 NLE 0.9332
40 264 0.9331
41 SSB 0.9322
42 AEF 0.9316
43 DGN 0.9314
44 S8V 0.9308
45 LDP 0.9306
46 PBN 0.9304
47 TYL 0.9304
48 258 0.9295
49 268 0.9295
50 XIZ 0.9290
51 2CO 0.9282
52 URP 0.9273
53 UN1 0.9272
54 SME 0.9265
55 ONL 0.9258
56 HCI 0.9258
57 GJZ 0.9257
58 PO6 0.9257
59 SHV 0.9256
60 MHO 0.9253
61 Q9Z 0.9249
62 I1E 0.9249
63 3PG 0.9243
64 HC4 0.9243
65 HIS 0.9240
66 SLZ 0.9239
67 SKJ 0.9237
68 SEP 0.9234
69 NNH 0.9225
70 RNS 0.9225
71 KMH 0.9217
72 6NA 0.9215
73 KDG 0.9213
74 3YP 0.9212
75 HSO 0.9210
76 DHY 0.9210
77 RNT 0.9207
78 GUA 0.9207
79 LT1 0.9207
80 PEA 0.9205
81 SD4 0.9201
82 PAC 0.9199
83 FEH 0.9198
84 YPN 0.9198
85 HPV 0.9198
86 PEL 0.9194
87 TZL 0.9193
88 PBA 0.9185
89 PHE 0.9185
90 YRL 0.9184
91 NMH 0.9181
92 MUC 0.9177
93 0L1 0.9175
94 HL5 0.9173
95 M4T 0.9171
96 16D 0.9170
97 NIZ 0.9157
98 O45 0.9155
99 FK8 0.9150
100 4HP 0.9150
101 ISZ 0.9144
102 49F 0.9144
103 B40 0.9141
104 AHN 0.9134
105 6XA 0.9133
106 4FA 0.9129
107 DHI 0.9129
108 MNN 0.9128
109 7BC 0.9125
110 PPY 0.9121
111 MEQ 0.9120
112 GVA 0.9120
113 ALA ALA 0.9119
114 COI 0.9118
115 HL4 0.9117
116 BHH 0.9115
117 AL0 0.9114
118 263 0.9112
119 3LR 0.9111
120 M45 0.9110
121 RUJ 0.9106
122 QY9 0.9104
123 OEG 0.9101
124 650 0.9101
125 OTR 0.9099
126 2FT 0.9099
127 LYN 0.9095
128 OAA 0.9095
129 CXP 0.9093
130 RBJ 0.9093
131 TZE 0.9090
132 0VT 0.9089
133 3HG 0.9088
134 HY1 0.9088
135 HG3 0.9086
136 SHO 0.9083
137 4TB 0.9077
138 13P 0.9075
139 F98 0.9070
140 GGB 0.9070
141 AEG 0.9067
142 IXW 0.9066
143 TIH 0.9065
144 NTU 0.9064
145 BHO 0.9061
146 HHI 0.9059
147 SDD 0.9056
148 OKG 0.9056
149 CXF 0.9055
150 NFA 0.9053
151 MSL 0.9051
152 LNR 0.9050
153 GPJ 0.9048
154 HSM 0.9045
155 HTX 0.9044
156 TAG 0.9044
157 GLY GLY 0.9043
158 E4P 0.9033
159 2EH 0.9033
160 3C4 0.9032
161 GPF 0.9032
162 DAL DAL 0.9031
163 ARG 0.9030
164 1L5 0.9030
165 PGH 0.9029
166 ZBT 0.9029
167 9ON 0.9026
168 42J 0.9026
169 FBJ 0.9022
170 MSE 0.9022
171 DHR 0.9020
172 BPW 0.9019
173 CEE 0.9019
174 URS 0.9017
175 QBM 0.9016
176 DHC 0.9015
177 54D 0.9014
178 HOC 0.9012
179 DZA 0.9012
180 DI6 0.9010
181 SHI 0.9010
182 PMF 0.9010
183 VKC 0.9008
184 P7Y 0.9007
185 SOR 0.9002
186 FUD 0.9000
187 HDH 0.8999
188 A29 0.8998
189 ENW 0.8998
190 CCE 0.8995
191 F9P 0.8994
192 GLO 0.8992
193 6JN 0.8989
194 XYL 0.8989
195 271 0.8987
196 069 0.8985
197 HPP 0.8984
198 NWH 0.8983
199 3HP 0.8982
200 OSE 0.8981
201 B3M 0.8980
202 TPA 0.8978
203 TYE 0.8978
204 173 0.8977
205 GRQ 0.8974
206 AT3 0.8974
207 XBT 0.8972
208 HGA 0.8970
209 BHL 0.8969
210 MLT 0.8969
211 3S5 0.8965
212 S2P 0.8964
213 NLP 0.8963
214 N9J 0.8961
215 NSD 0.8955
216 I4B 0.8955
217 J9N 0.8954
218 B3U 0.8953
219 2HC 0.8951
220 PG0 0.8951
221 OCT 0.8950
222 OC9 0.8949
223 KPA 0.8945
224 HFA 0.8944
225 64Z 0.8943
226 36M 0.8942
227 5FX 0.8941
228 9J3 0.8938
229 1BN 0.8933
230 G3H 0.8932
231 QMP 0.8932
232 CS2 0.8930
233 DXG 0.8928
234 XLS 0.8926
235 GCO 0.8925
236 EOU 0.8925
237 3QM 0.8924
238 RBL 0.8924
239 MD0 0.8924
240 OHP 0.8923
241 DHM 0.8922
242 G3P 0.8920
243 AE3 0.8919
244 RMN 0.8917
245 HPS 0.8915
246 9SE 0.8914
247 2FM 0.8912
248 2LP 0.8910
249 R2P 0.8910
250 PZI 0.8905
251 GP9 0.8905
252 BSX 0.8904
253 FOM 0.8901
254 AHC 0.8901
255 DAR 0.8899
256 129 0.8897
257 I38 0.8896
258 41K 0.8891
259 8GL 0.8891
260 GLR 0.8891
261 M3P 0.8891
262 HCS 0.8889
263 F06 0.8889
264 CIR 0.8888
265 4SD 0.8887
266 DLT 0.8884
267 4LR 0.8883
268 FBM 0.8881
269 LUQ 0.8881
270 LPK 0.8880
271 M3H 0.8878
272 MTL 0.8877
273 MES 0.8876
274 KTA 0.8871
275 3BU 0.8871
276 M6H 0.8870
277 K6V 0.8869
278 LTL 0.8866
279 TEO 0.8863
280 JZ4 0.8862
281 CCD 0.8861
282 5XB 0.8860
283 69O 0.8859
284 TZP 0.8855
285 MZT 0.8854
286 51F 0.8852
287 SYM 0.8850
288 XYH 0.8847
289 1N5 0.8846
290 0OC 0.8844
291 MPJ 0.8841
292 P58 0.8841
293 HMS 0.8840
294 GLY ALA 0.8840
295 ILO 0.8838
296 2JJ 0.8838
297 DAV 0.8835
298 ENV 0.8829
299 7N0 0.8828
300 8EW 0.8827
301 FOC 0.8825
302 152 0.8822
303 7WG 0.8822
304 1X4 0.8814
305 SOL 0.8813
306 NPI 0.8811
307 IOM 0.8810
308 GWM 0.8808
309 DER 0.8807
310 OHJ 0.8807
311 LVD 0.8807
312 PRO GLY 0.8805
313 5WZ 0.8804
314 3GZ 0.8801
315 1GP 0.8801
316 Q07 0.8796
317 5OY 0.8794
318 FP1 0.8793
319 MAH 0.8792
320 JFJ 0.8790
321 NFM 0.8785
322 HXY 0.8783
323 L99 0.8779
324 8U3 0.8778
325 1LN 0.8773
326 8SZ 0.8773
327 RAT 0.8769
328 IP8 0.8769
329 OYA 0.8766
330 PJL 0.8766
331 CHH 0.8762
332 9X7 0.8761
333 QUS 0.8760
334 DYT 0.8759
335 AFS 0.8757
336 NCT 0.8757
337 HBU 0.8756
338 7UC 0.8753
339 BRH 0.8750
340 TSS 0.8749
341 F90 0.8747
342 MLY 0.8746
343 6HN 0.8745
344 AJ3 0.8740
345 PSJ 0.8739
346 DEZ 0.8737
347 261 0.8736
348 PML 0.8733
349 TPO 0.8729
350 ENO 0.8728
351 M1T 0.8722
352 4TP 0.8713
353 LFC 0.8710
354 JZ7 0.8710
355 FXY 0.8707
356 KPC 0.8705
357 API 0.8704
358 Q06 0.8703
359 BHU 0.8699
360 TZM 0.8698
361 HJH 0.8696
362 DPF 0.8695
363 HIC 0.8693
364 CSS 0.8692
365 3MV 0.8692
366 DEE 0.8692
367 X1R 0.8692
368 RTK 0.8691
369 YIE 0.8689
370 56D 0.8689
371 1H1 0.8687
372 LL2 0.8685
373 61M 0.8685
374 PRY 0.8684
375 SR1 0.8680
376 4ZD 0.8679
377 SHA 0.8678
378 EHM 0.8674
379 HPL 0.8673
380 3QO 0.8668
381 IVL 0.8664
382 8XL 0.8659
383 RP5 0.8658
384 MF3 0.8655
385 CFA 0.8655
386 ACH 0.8654
387 Z70 0.8625
388 HF2 0.8625
389 EN1 0.8623
390 2RH 0.8618
391 2D8 0.8607
392 SG3 0.8598
393 GVM 0.8585
394 XQI 0.8582
395 6Q3 0.8570
396 XRX 0.8564
397 FF3 0.8551
398 1DU 0.8546
399 EGV 0.8540
400 266 0.8533
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GZ6; Ligand: NDP; 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: 5gz6.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5GZ6; Ligand: 7C3; 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: 5gz6.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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