Receptor
PDB id Resolution Class Description Source Keywords
4JDC 1.6 Å EC: 1.5.1.12 CRYSTAL STRUCTURE OF THE DELTA-PYRROLINE-5-CARBOXYLATE DEHYD FROM MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS PYRROLINE-5-CARBOXYLATE DEHYDROGENASE ALDEHYDE DEHYDROGENASOXYDOREDUCTION OXIDOREDUCTASE
Ref.: CHARACTERIZATION OF THE PROLINE-UTILIZATION PATHWAY MYCOBACTERIUM TUBERCULOSIS THROUGH STRUCTURAL AND F STUDIES. ACTA CRYSTALLOGR.,SECT.D V. 70 968 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:601;
Valid;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4NS3 2.38 Å EC: 1.5.1.12 CRYSTAL STRUCTURE OF THE DELTA-PYRROLINE-5-CARBOXYLATE DEHYD FROM MYCOBACTERIUM TUBERCULOSIS BOUND WITH NAD AND COBALAMI MYCOBACTERIUM TUBERCULOSIS ROSSMANN FOLD DEHYDROGENASE OXIDOREDUCTASE DEHYDROGENATIO
Ref.: USE OF A "SILVER BULLET" TO RESOLVE CRYSTAL LATTICE DISLOCATION DISORDER: A COBALAMIN COMPLEX OF DELTA (1)-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM MYCO TUBERCULOSIS. J.STRUCT.BIOL. V. 189 153 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4NS3 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 4IHI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 4JDC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4NS3 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 4IHI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 4JDC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4NS3 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 4IHI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 4JDC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3V9L - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 4LH1 - MLA C3 H4 O4 C(C(=O)O)C....
6 4LH0 - GLV C2 H2 O3 C(=O)C(=O)....
7 3V9K - GLU C5 H9 N O4 C(CC(=O)O)....
8 4LH2 Ki = 58 mM SIN C4 H6 O4 O=C([O-])C....
9 4LH3 Ki = 30 mM GUA C5 H8 O4 C(CC(=O)O)....
10 4OE4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAD; Similar ligands found: 220
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NAD IBO 0.845455 0.933333
3 NHD 0.821429 0.972222
4 NAP 0.811966 0.986111
5 NAJ PYZ 0.803419 0.910256
6 NFD 0.791304 0.946667
7 NXX 0.765766 0.972603
8 DND 0.765766 0.972603
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 AMP NAD 0.696 0.945946
15 NDE 0.689922 0.972603
16 NAJ 0.683333 0.972222
17 NDC 0.679389 0.934211
18 NDO 0.674603 0.958904
19 N01 0.656 0.972222
20 CNA 0.642276 0.972603
21 NBP 0.621212 0.922078
22 NAD BBN 0.609929 0.876543
23 8ID 0.609756 0.922078
24 NAD CJ3 0.601399 0.845238
25 ADP MG 0.579439 0.918919
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BEF ADP 0.574074 0.894737
30 ADP BEF 0.574074 0.894737
31 BA3 0.566038 0.958333
32 NAD NDT 0.565789 0.755319
33 M33 0.564815 0.918919
34 ADP PO3 0.563636 0.957747
35 B4P 0.560748 0.958333
36 AP5 0.560748 0.958333
37 ATP MG 0.558559 0.918919
38 AN2 0.555556 0.918919
39 GAP 0.553571 0.932432
40 OOB 0.551724 0.972222
41 CA0 0.550459 0.932432
42 ATP 0.545455 0.931507
43 ACP 0.545455 0.906667
44 NAD TDB 0.544872 0.70297
45 ADP ALF 0.54386 0.883117
46 ALF ADP 0.54386 0.883117
47 5FA 0.540541 0.931507
48 AQP 0.540541 0.931507
49 APR 0.540541 0.931507
50 AR6 0.540541 0.931507
51 ANP MG 0.53913 0.907895
52 VO4 ADP 0.53913 0.945205
53 ADP VO4 0.53913 0.945205
54 AGS 0.535714 0.883117
55 SAP 0.535714 0.883117
56 AD9 0.535714 0.906667
57 WAQ 0.533333 0.896104
58 ABM 0.53271 0.905405
59 00A 0.529412 0.921053
60 DLL 0.529412 0.972222
61 ANP 0.526316 0.906667
62 NJP 0.526316 0.959459
63 ACQ 0.526316 0.906667
64 OAD 0.525 0.932432
65 AMP MG 0.523364 0.905405
66 ADX 0.522523 0.839506
67 5AL 0.521739 0.945205
68 A1R 0.521008 0.871795
69 9SN 0.520325 0.909091
70 AMP 0.518868 0.930556
71 A 0.518868 0.930556
72 50T 0.517857 0.893333
73 ATF 0.517241 0.894737
74 DAL AMP 0.516949 0.945205
75 3OD 0.516393 0.932432
76 1ZZ 0.516393 0.851852
77 SON 0.513514 0.92
78 PRX 0.513274 0.881579
79 SRP 0.512821 0.92
80 ADP BMA 0.512397 0.932432
81 3UK 0.512397 0.958904
82 MYR AMP 0.512195 0.851852
83 NAJ PZO 0.510949 0.909091
84 NMN 0.509434 0.875
85 AMP DBH 0.507937 0.906667
86 A22 0.504202 0.945205
87 FA5 0.504 0.945946
88 ATP A A A 0.504 0.971831
89 TYR AMP 0.5 0.945946
90 8QN 0.5 0.945205
91 NAX 0.496183 0.886076
92 PR8 0.495935 0.8625
93 PAJ 0.495868 0.873418
94 4AD 0.495868 0.933333
95 AMO 0.495868 0.92
96 ADQ 0.495868 0.932432
97 A12 0.495495 0.894737
98 AP2 0.495495 0.894737
99 ALF ADP 3PG 0.492424 0.873418
100 LA8 ALF 3PG 0.492424 0.873418
101 AHZ 0.492308 0.851852
102 YAP 0.492063 0.933333
103 FYA 0.491935 0.918919
104 AHX 0.491803 0.884615
105 4UU 0.488372 0.933333
106 5SV 0.487603 0.8375
107 TAT 0.487179 0.894737
108 APC 0.486957 0.894737
109 SRA 0.486239 0.881579
110 NAI 0.484848 0.921053
111 6V0 0.484848 0.909091
112 GTA 0.484615 0.898734
113 A A 0.483871 0.958333
114 LAD 0.483871 0.873418
115 AU1 0.482456 0.906667
116 TXE 0.481203 0.921053
117 AF3 ADP 3PG 0.481203 0.873418
118 OMR 0.481203 0.841463
119 LAQ 0.480916 0.851852
120 G3A 0.48062 0.909091
121 TXA 0.48 0.92
122 NB8 0.48 0.884615
123 ME8 0.48 0.851852
124 BIS 0.48 0.871795
125 PTJ 0.48 0.884615
126 139 0.477941 0.886076
127 LPA AMP 0.477273 0.851852
128 AR6 AR6 0.476923 0.958333
129 G5P 0.476923 0.909091
130 AFH 0.476923 0.873418
131 25L 0.47619 0.945205
132 25A 0.47541 0.958333
133 DZD 0.47482 0.897436
134 TXD 0.473684 0.921053
135 4UV 0.472868 0.933333
136 TYM 0.470149 0.945946
137 ADV 0.470085 0.894737
138 RBY 0.470085 0.894737
139 ARG AMP 0.469697 0.841463
140 4TA 0.467626 0.864198
141 48N 0.466165 0.884615
142 XAH 0.465116 0.851852
143 4UW 0.462687 0.897436
144 M24 0.461538 0.886076
145 IOT 0.459854 0.821429
146 T5A 0.456522 0.853659
147 EAD 0.455782 0.886076
148 MAP 0.455285 0.883117
149 BT5 0.453901 0.821429
150 A4P 0.452555 0.833333
151 UP5 0.451852 0.933333
152 PAP 0.445378 0.917808
153 AP0 0.445255 0.884615
154 4TC 0.445255 0.909091
155 YLP 0.444444 0.831325
156 P1H 0.443709 0.864198
157 AOC 0.442478 0.810811
158 Z5A 0.439189 0.833333
159 2A5 0.436975 0.857143
160 G A A A 0.43662 0.909091
161 COD 0.43662 0.802326
162 ADJ 0.435714 0.841463
163 YLC 0.434783 0.851852
164 YLB 0.434783 0.831325
165 U A G G 0.433566 0.921053
166 ATR 0.433333 0.90411
167 7MD 0.432836 0.851852
168 G5A 0.429752 0.790698
169 PO4 PO4 A A A A PO4 0.429688 0.943662
170 TAD 0.42963 0.873418
171 5AS 0.42735 0.770115
172 BTX 0.426573 0.831325
173 YLA 0.425532 0.831325
174 DSZ 0.425197 0.790698
175 NCN 0.424779 0.805556
176 UPA 0.42446 0.921053
177 VMS 0.424 0.8
178 54H 0.424 0.8
179 N0B 0.422819 0.853659
180 6AD 0.422764 0.85
181 AYB 0.422535 0.821429
182 7D3 0.422414 0.844156
183 YLY 0.421769 0.821429
184 TSB 0.420635 0.809524
185 ODP 0.41958 0.922078
186 AV2 0.419355 0.855263
187 FB0 0.419355 0.775281
188 A5A 0.419355 0.819277
189 NNR 0.419048 0.739726
190 A A A 0.418605 0.918919
191 LEU LMS 0.418605 0.793103
192 649 0.417266 0.775281
193 NMN AMP PO4 0.416667 0.933333
194 SSA 0.416 0.790698
195 P5A 0.415385 0.755556
196 LSS 0.414062 0.772727
197 A2R 0.412698 0.918919
198 52H 0.412698 0.790698
199 JB6 0.412214 0.896104
200 5N5 0.411215 0.783784
201 YSA 0.410448 0.811765
202 5CA 0.409449 0.790698
203 53H 0.409449 0.790698
204 ITT 0.408333 0.878378
205 7D4 0.408333 0.844156
206 NA7 0.407692 0.894737
207 5CD 0.407407 0.794521
208 0WD 0.406897 0.909091
209 A3P 0.40678 0.930556
210 AVV 0.40625 0.860759
211 RAB 0.40566 0.808219
212 ADN 0.40566 0.808219
213 XYA 0.40566 0.808219
214 FDA 0.405063 0.823529
215 GSU 0.40458 0.790698
216 7MC 0.404255 0.831325
217 NSS 0.403101 0.811765
218 6FA 0.402516 0.853659
219 NVA LMS 0.4 0.793103
220 PPS 0.4 0.817073
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NS3; Ligand: NAD; Similar sites found: 66
This union binding pocket(no: 1) in the query (biounit: 4ns3.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.009585 0.42402 None
2 2GU8 796 0.03689 0.40144 1.48368
3 1IXE CIT 0.0167 0.41085 1.85676
4 4WOE ADP 0.007545 0.4287 2.13144
5 2CDU FAD 0.02119 0.40051 2.21239
6 3BRE C2E 0.005962 0.43667 2.23464
7 2BIF BOG 0.007117 0.40349 2.77186
8 2BIF SIN 0.02389 0.40277 2.77186
9 5MRH Q9Z 0.00513 0.43062 2.84192
10 3QDK QDK 0.01558 0.41615 2.84192
11 5TVA AMP 0.009859 0.40806 2.91667
12 1YQZ FAD 0.04693 0.40016 2.96804
13 1T36 U 0.001619 0.42749 3.19716
14 5EW9 5VC 0.02124 0.43362 3.32103
15 5BVE 4VG 0.01562 0.42314 3.3241
16 3OV6 MK0 0.009326 0.41012 3.52645
17 4DSU BZI 0.002441 0.45423 3.7037
18 4R84 CSF 0.003337 0.40449 4.17495
19 1CLU DBG 0.02158 0.40396 4.81928
20 4WCX MET 0.001114 0.46109 4.97336
21 2Z4T C5P 0.01506 0.40325 5.05837
22 4OYA 1VE 0.01428 0.42701 5.10638
23 4JCA CIT 0.001418 0.47265 5.98802
24 2IDO TMP 0.02209 0.40557 6.98925
25 1KZL CRM 0.009742 0.41242 7.69231
26 5XDT MB3 0.008132 0.41649 7.79221
27 1EZ0 NAP 0.000005541 0.45167 7.84314
28 2G30 ALA ALA PHE 0.001173 0.41209 8.13953
29 4NS0 PIO 0.0219 0.4001 8.27068
30 2GNM MAN 0.01615 0.40912 8.73016
31 1I7M CG 0.005996 0.42726 8.95522
32 5L2J 6UL 0.01696 0.42395 9.18367
33 5L2J 70E 0.01795 0.42395 9.18367
34 4XMF HSM 0.001075 0.44729 9.23913
35 5JFL NAD 0.000009421 0.54362 9.73282
36 3LXK MI1 0.008665 0.40754 10.7034
37 3EJ0 11X 0.01485 0.42477 11.2245
38 2XG5 EC2 0.002992 0.45188 11.9266
39 2XG5 EC5 0.002992 0.45188 11.9266
40 3U4L ATP 0.007979 0.40132 12.8571
41 3G08 FEE 0.02721 0.40791 15.1515
42 5TVF CGQ 0.01329 0.41009 18.8235
43 2Y5D NAP 0.0000002613 0.5066 22.8464
44 3VZ3 NAP 0.0000001534 0.62835 28.0639
45 3VZ3 SSN 0.00000023 0.62815 28.0639
46 1T90 NAD 0.00000009124 0.63859 30.0412
47 4I3V NAD 0.000000003289 0.5403 30.7377
48 3EFV NAD 0.0000003359 0.60873 30.9524
49 1O9J NAD 0.000000008688 0.68254 35.1297
50 4ZUL UN1 0.0000001472 0.49871 35.4776
51 5L13 6ZE 0.00000006945 0.41338 35.5899
52 5UCD NAP 0.0000002102 0.51721 36.3239
53 2WOX NDP 0.00000001585 0.67956 36.4008
54 3IWJ NAD 0.0000000006282 0.68938 36.4121
55 2WME NAP 0.00000008096 0.61208 36.5306
56 4PZ2 NAD 0.000000006709 0.53378 36.7041
57 4YWV SSN 0.000001144 0.5888 36.7742
58 4A0M NAD 0.000000008063 0.68636 36.9449
59 3RHJ NAP 0.000000008857 0.69724 37.3002
60 4I8P NAD 0.000000001992 0.71861 37.3077
61 4I9B NAD 0.000000001148 0.6739 38.4913
62 3IWK NAD 0.000009191 0.50352 38.5686
63 5KF6 NAD 0.0000000004579 0.74535 38.7211
64 3JZ4 NAP 0.000000009771 0.67272 40.5405
65 2QE0 NAP 0.00000001912 0.4645 44.2105
66 2IMP NAI 0.01785 0.4563 45.5115
Pocket No.: 2; Query (leader) PDB : 4NS3; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4ns3.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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