Receptor
PDB id Resolution Class Description Source Keywords
5X9D 2.1 Å EC: 1.1.1.3 CRYSTAL STRUCTURE OF HOMOSERINE DEHYDROGENASE IN COMPLEX WIT CYSTEINE AND NAD SULFOLOBUS TOKODAII (STRAIN DSM 16993 10545 / NBRC 100140 / 7) OXIDOREDUCTASE COMPLEX INHIBITOR
Ref.: INHIBITION OF HOMOSERINE DEHYDROGENASE BY FORMATION CYSTEINE-NAD COVALENT COMPLEX SCI REP V. 8 5749 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
80F A:501;
Valid;
none;
submit data
784.583 C24 H34 N8 O16 P2 S c1nc(...
TLA A:502;
Invalid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X9D 2.1 Å EC: 1.1.1.3 CRYSTAL STRUCTURE OF HOMOSERINE DEHYDROGENASE IN COMPLEX WIT CYSTEINE AND NAD SULFOLOBUS TOKODAII (STRAIN DSM 16993 10545 / NBRC 100140 / 7) OXIDOREDUCTASE COMPLEX INHIBITOR
Ref.: INHIBITION OF HOMOSERINE DEHYDROGENASE BY FORMATION CYSTEINE-NAD COVALENT COMPLEX SCI REP V. 8 5749 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5X9D - 80F C24 H34 N8 O16 P2 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5X9D - 80F C24 H34 N8 O16 P2 S c1nc(c2c(n....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6A0T - HSE C4 H9 N O3 C(CO)[C@@H....
2 6A0U - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 6A0S Kd = 1.6 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 5X9D - 80F C24 H34 N8 O16 P2 S c1nc(c2c(n....
5 4XB2 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
6 4XB1 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 80F; Similar ligands found: 245
No: Ligand ECFP6 Tc MDL keys Tc
1 80F 1 1
2 NAI 0.65 0.925926
3 EAD 0.636364 0.915663
4 P1H 0.617647 0.894118
5 AP0 0.612903 0.891566
6 A2D 0.596154 0.864198
7 NAJ PZO 0.59542 0.869048
8 NAJ PYZ 0.577778 0.829545
9 6V0 0.571429 0.914634
10 NAX 0.571429 0.939024
11 TXD 0.571429 0.857143
12 BA3 0.570093 0.864198
13 TXE 0.566929 0.879518
14 B4P 0.564815 0.864198
15 AP5 0.564815 0.864198
16 ADP 0.564815 0.841463
17 HEJ 0.563636 0.841463
18 ATP 0.563636 0.841463
19 KG4 0.563636 0.865854
20 AN2 0.559633 0.831325
21 5FA 0.558559 0.841463
22 AR6 0.558559 0.864198
23 AQP 0.558559 0.841463
24 APR 0.558559 0.864198
25 SRP 0.556522 0.878049
26 5AL 0.552632 0.853659
27 HQG 0.551724 0.853659
28 AMO 0.550847 0.901235
29 A1R 0.550847 0.835294
30 ACP 0.54955 0.843373
31 0WD 0.548872 0.914634
32 A22 0.547009 0.853659
33 DG1 0.546763 0.914634
34 1DG 0.546763 0.914634
35 AT4 0.545455 0.855422
36 ANP 0.54386 0.821429
37 ACQ 0.54386 0.843373
38 M33 0.540541 0.831325
39 CA0 0.540541 0.865854
40 SAP 0.539823 0.845238
41 AGS 0.539823 0.845238
42 AD9 0.539823 0.821429
43 NDP 0.537879 0.914634
44 ADJ 0.537879 0.872093
45 ADQ 0.537815 0.865854
46 4AD 0.537815 0.890244
47 50T 0.535714 0.809524
48 8LQ 0.533898 0.855422
49 ME8 0.532787 0.83908
50 YAP 0.532258 0.890244
51 PRX 0.530973 0.77907
52 8LH 0.529915 0.833333
53 6YZ 0.529915 0.843373
54 8QN 0.529412 0.853659
55 OAD 0.528926 0.865854
56 ADX 0.526786 0.786517
57 LAD 0.52459 0.837209
58 A 0.523364 0.817073
59 AMP 0.523364 0.817073
60 UP5 0.523077 0.890244
61 ATF 0.521368 0.811765
62 AHX 0.520661 0.847059
63 NB8 0.520325 0.869048
64 PTJ 0.520325 0.804598
65 3OD 0.520325 0.865854
66 FA5 0.52 0.901235
67 F2R 0.518519 0.820225
68 9X8 0.516393 0.86747
69 4TC 0.515152 0.891566
70 8LE 0.512821 0.823529
71 A3R 0.512397 0.835294
72 PAJ 0.512397 0.816092
73 WAQ 0.512195 0.835294
74 NXX 0.51145 0.878049
75 DND 0.51145 0.878049
76 00A 0.508197 0.835294
77 TXA 0.508065 0.855422
78 APC 0.504348 0.833333
79 OOB 0.504132 0.876543
80 25L 0.504 0.853659
81 48N 0.503817 0.847059
82 DQV 0.5 0.876543
83 TYM 0.496241 0.901235
84 OMR 0.496241 0.788889
85 B5M 0.496063 0.845238
86 BIS 0.496 0.793103
87 ABM 0.495495 0.797619
88 45A 0.495495 0.797619
89 YLP 0.492424 0.8
90 XAH 0.492188 0.797753
91 5SV 0.491803 0.744444
92 25A 0.491803 0.841463
93 TAT 0.491525 0.855422
94 T99 0.491525 0.855422
95 TYR AMP 0.488372 0.86747
96 9SN 0.488189 0.825581
97 PR8 0.488 0.827586
98 A12 0.486726 0.833333
99 AP2 0.486726 0.833333
100 1ZZ 0.484127 0.777778
101 FYA 0.484127 0.853659
102 DLL 0.483871 0.876543
103 DAL AMP 0.483607 0.831325
104 5X8 0.482759 0.768293
105 YLA 0.481752 0.820225
106 YLB 0.481481 0.8
107 YLC 0.481481 0.83908
108 AFH 0.480916 0.837209
109 3UK 0.48 0.865854
110 9ZD 0.479675 0.813953
111 9ZA 0.479675 0.813953
112 OZV 0.479675 0.841463
113 AYB 0.478261 0.791209
114 ADP MG 0.478261 0.817073
115 CNA 0.478261 0.878049
116 NZQ 0.478261 0.926829
117 SRA 0.477477 0.821429
118 B5V 0.47619 0.855422
119 RBY 0.474576 0.855422
120 ADV 0.474576 0.855422
121 AU1 0.474138 0.821429
122 COD 0.471429 0.793478
123 139 0.471014 0.870588
124 NPW 0.471014 0.927711
125 T5A 0.471014 0.905882
126 7MD 0.469697 0.83908
127 NAQ 0.468966 0.804598
128 TXP 0.467626 0.847059
129 A4P 0.467153 0.842697
130 GAP 0.466667 0.821429
131 4UV 0.465649 0.91358
132 SON 0.465517 0.855422
133 ATP MG 0.462185 0.817073
134 APC MG 0.462185 0.797619
135 ADP PO3 0.462185 0.817073
136 G3A 0.462121 0.825581
137 B5Y 0.461538 0.845238
138 NMN AMP PO4 0.460993 0.890244
139 NAD 0.460993 0.853659
140 UPA 0.459854 0.879518
141 ARG AMP 0.458647 0.788889
142 G5P 0.458647 0.825581
143 ADP BMA 0.456693 0.843373
144 GTA 0.455224 0.797753
145 A3D 0.454545 0.843373
146 IOT 0.453237 0.791209
147 LAQ 0.451852 0.818182
148 A2R 0.451613 0.853659
149 MAP 0.448 0.802326
150 4UU 0.447761 0.91358
151 NDE 0.447368 0.833333
152 ADP ALF 0.447154 0.761364
153 ALF ADP 0.447154 0.761364
154 N0B 0.445946 0.840909
155 SFG 0.445378 0.73494
156 NJP 0.443662 0.845238
157 VO4 ADP 0.443548 0.809524
158 ADP VO4 0.443548 0.809524
159 NAE 0.442177 0.823529
160 2A5 0.441667 0.8
161 FB0 0.441558 0.75
162 EEM 0.439024 0.681319
163 7MC 0.438849 0.820225
164 ATR 0.438017 0.817073
165 DZD 0.4375 0.837209
166 GA7 0.437037 0.833333
167 7D4 0.436975 0.767442
168 ZID 0.436242 0.843373
169 YLY 0.435374 0.791209
170 MYR AMP 0.435115 0.758242
171 62F 0.434783 0.797753
172 4UW 0.434783 0.880952
173 SAI 0.434426 0.72093
174 SAH 0.434426 0.75
175 NA7 0.434109 0.833333
176 TAD 0.433824 0.858824
177 5AS 0.432203 0.708333
178 S7M 0.432 0.7
179 SSA 0.432 0.782609
180 AF3 ADP 3PG 0.431655 0.795455
181 XNP 0.430556 0.892857
182 LMS 0.429825 0.747253
183 DSZ 0.429688 0.802198
184 LSS 0.429688 0.747368
185 BT5 0.427586 0.831461
186 7D3 0.42735 0.767442
187 NVA LMS 0.426357 0.739583
188 SA8 0.42623 0.696629
189 PAP 0.42623 0.829268
190 FNK 0.425926 0.826087
191 M24 0.425676 0.806818
192 YSA 0.425373 0.782609
193 TSB 0.425197 0.76087
194 53H 0.425197 0.726316
195 5CA 0.425197 0.782609
196 ITT 0.425 0.795181
197 A5A 0.424 0.75
198 LEU LMS 0.423077 0.739583
199 AOC 0.422414 0.73494
200 BTX 0.42069 0.820225
201 SMM 0.420635 0.695652
202 GSU 0.419847 0.782609
203 A A 0.419847 0.819277
204 SFD 0.41875 0.757576
205 NSS 0.418605 0.782609
206 VMS 0.417323 0.734043
207 52H 0.417323 0.726316
208 54H 0.417323 0.734043
209 JB6 0.416667 0.857143
210 6AD 0.416 0.837209
211 NDC 0.414013 0.804598
212 ODP 0.413793 0.858824
213 JSQ 0.41129 0.802326
214 HFD 0.41129 0.802326
215 G5A 0.41129 0.763441
216 ADN 0.411215 0.731707
217 XYA 0.411215 0.731707
218 RAB 0.411215 0.731707
219 AHZ 0.410072 0.797753
220 KAA 0.409091 0.739583
221 J4G 0.409091 0.86747
222 FDA 0.408805 0.833333
223 3AT 0.408 0.841463
224 0UM 0.407692 0.688889
225 ATP A 0.407407 0.829268
226 ATP A A A 0.407407 0.829268
227 LPA AMP 0.407143 0.797753
228 6FA 0.40625 0.8
229 AR6 AR6 0.405797 0.841463
230 PPS 0.404762 0.766667
231 7D5 0.403509 0.744186
232 AV2 0.401575 0.776471
233 K15 0.401515 0.673913
234 AMP DBH 0.40146 0.821429
235 WSA 0.401408 0.791209
236 4TA 0.401361 0.872093
237 AMP NAD 0.401361 0.853659
238 FAD 0.401235 0.808989
239 FAS 0.401235 0.808989
240 F2N 0.401163 0.835165
241 A3P 0.4 0.817073
242 3DH 0.4 0.694118
243 5CD 0.4 0.698795
244 AVV 0.4 0.804598
245 A2P 0.4 0.804878
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X9D; Ligand: 80F; 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: 5x9d.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5X9D; Ligand: 80F; 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: 5x9d.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
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