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 (2D)
Ligand no: 1; Ligand: 80F; Similar ligands found: 253
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 NDP DTT 0.608696 0.928571
7 A2D 0.596154 0.864198
8 NAJ PZO 0.59542 0.869048
9 NAJ PYZ 0.577778 0.829545
10 TXD 0.571429 0.857143
11 6V0 0.571429 0.914634
12 NAX 0.571429 0.939024
13 BA3 0.570093 0.864198
14 TXE 0.566929 0.879518
15 AP5 0.564815 0.864198
16 B4P 0.564815 0.864198
17 ADP 0.564815 0.841463
18 KG4 0.563636 0.865854
19 HEJ 0.563636 0.841463
20 ATP 0.563636 0.841463
21 AN2 0.559633 0.831325
22 AQP 0.558559 0.841463
23 AR6 0.558559 0.864198
24 APR 0.558559 0.864198
25 5FA 0.558559 0.841463
26 SRP 0.556522 0.878049
27 5AL 0.552632 0.853659
28 HQG 0.551724 0.853659
29 A1R 0.550847 0.835294
30 AMO 0.550847 0.901235
31 ACP 0.54955 0.843373
32 0WD 0.548872 0.914634
33 A22 0.547009 0.853659
34 DG1 0.546763 0.914634
35 1DG 0.546763 0.914634
36 AT4 0.545455 0.855422
37 ANP 0.54386 0.821429
38 ACQ 0.54386 0.843373
39 M33 0.540541 0.831325
40 CA0 0.540541 0.865854
41 AGS 0.539823 0.845238
42 AD9 0.539823 0.821429
43 ADJ 0.537879 0.872093
44 NDP 0.537879 0.914634
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 PRX 0.530973 0.77907
51 8LH 0.529915 0.833333
52 6YZ 0.529915 0.843373
53 8QN 0.529412 0.853659
54 OAD 0.528926 0.865854
55 ADX 0.526786 0.786517
56 LAD 0.52459 0.837209
57 A 0.523364 0.817073
58 AMP 0.523364 0.817073
59 UP5 0.523077 0.890244
60 ATF 0.521368 0.811765
61 QA7 0.521008 0.823529
62 JNT 0.520661 0.843373
63 AHX 0.520661 0.847059
64 3OD 0.520325 0.865854
65 PTJ 0.520325 0.804598
66 NB8 0.520325 0.869048
67 FA5 0.52 0.901235
68 F2R 0.518519 0.820225
69 9X8 0.516393 0.86747
70 4TC 0.515152 0.891566
71 8LE 0.512821 0.823529
72 PAJ 0.512397 0.816092
73 A3R 0.512397 0.835294
74 WAQ 0.512195 0.835294
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 L3W 0.503759 0.901235
83 DQV 0.5 0.876543
84 OMR 0.496241 0.788889
85 TYM 0.496241 0.901235
86 B5M 0.496063 0.845238
87 BIS 0.496 0.793103
88 45A 0.495495 0.797619
89 ABM 0.495495 0.797619
90 YLP 0.492424 0.8
91 XAH 0.492188 0.797753
92 5SV 0.491803 0.744444
93 25A 0.491803 0.841463
94 T99 0.491525 0.855422
95 TAT 0.491525 0.855422
96 AMP MG 0.490909 0.804878
97 9SN 0.488189 0.825581
98 PR8 0.488 0.827586
99 V2G 0.487395 0.825581
100 A12 0.486726 0.833333
101 AP2 0.486726 0.833333
102 KMQ 0.484375 0.855422
103 FYA 0.484127 0.853659
104 1ZZ 0.484127 0.777778
105 DLL 0.483871 0.876543
106 DAL AMP 0.483607 0.831325
107 5X8 0.482759 0.768293
108 YLA 0.481752 0.820225
109 YLB 0.481481 0.8
110 YLC 0.481481 0.83908
111 AFH 0.480916 0.837209
112 3UK 0.48 0.865854
113 OZV 0.479675 0.841463
114 9ZD 0.479675 0.813953
115 9ZA 0.479675 0.813953
116 ADP MG 0.478261 0.817073
117 ADP BEF 0.478261 0.817073
118 NZQ 0.478261 0.926829
119 AYB 0.478261 0.791209
120 CNA 0.478261 0.878049
121 SRA 0.477477 0.821429
122 B5V 0.47619 0.855422
123 ADV 0.474576 0.855422
124 RBY 0.474576 0.855422
125 AU1 0.474138 0.821429
126 COD 0.471429 0.793478
127 T5A 0.471014 0.905882
128 NPW 0.471014 0.927711
129 139 0.471014 0.870588
130 7MD 0.469697 0.83908
131 NAQ 0.468966 0.804598
132 TXP 0.467626 0.847059
133 A4P 0.467153 0.842697
134 GAP 0.466667 0.821429
135 4UV 0.465649 0.91358
136 SON 0.465517 0.855422
137 APC MG 0.462185 0.797619
138 ADP PO3 0.462185 0.817073
139 ATP MG 0.462185 0.817073
140 G3A 0.462121 0.825581
141 B5Y 0.461538 0.845238
142 NAD 0.460993 0.853659
143 NMN AMP PO4 0.460993 0.890244
144 UPA 0.459854 0.879518
145 ANP MG 0.459016 0.809524
146 VO4 ADP 0.459016 0.8
147 ARG AMP 0.458647 0.788889
148 G5P 0.458647 0.825581
149 BEF ADP 0.458333 0.797619
150 ADP BMA 0.456693 0.843373
151 GTA 0.455224 0.797753
152 A3D 0.454545 0.843373
153 IOT 0.453237 0.791209
154 LAQ 0.451852 0.818182
155 A2R 0.451613 0.853659
156 MAP 0.448 0.802326
157 4UU 0.447761 0.91358
158 NDE 0.447368 0.833333
159 ALF ADP 0.447154 0.761364
160 N0B 0.445946 0.840909
161 SFG 0.445378 0.73494
162 LEU LMS 0.445312 0.736842
163 NJP 0.443662 0.845238
164 NAE 0.442177 0.823529
165 D4F 0.442177 0.860465
166 ALF ADP 3PG 0.442029 0.795455
167 2A5 0.441667 0.8
168 FB0 0.441558 0.75
169 EEM 0.439024 0.681319
170 7MC 0.438849 0.820225
171 ATR 0.438017 0.817073
172 DZD 0.4375 0.837209
173 GA7 0.437037 0.833333
174 7D4 0.436975 0.767442
175 ZID 0.436242 0.843373
176 YLY 0.435374 0.791209
177 MYR AMP 0.435115 0.758242
178 62F 0.434783 0.797753
179 4UW 0.434783 0.880952
180 SAH 0.434426 0.75
181 SAI 0.434426 0.72093
182 NA7 0.434109 0.833333
183 TAD 0.433824 0.858824
184 5AS 0.432203 0.708333
185 S7M 0.432 0.7
186 SSA 0.432 0.782609
187 AF3 ADP 3PG 0.431655 0.795455
188 XNP 0.430556 0.892857
189 LMS 0.429825 0.747253
190 LSS 0.429688 0.747368
191 DSZ 0.429688 0.802198
192 NAD TDB 0.428571 0.841463
193 NAD IBO 0.428571 0.841463
194 BT5 0.427586 0.831461
195 7D3 0.42735 0.767442
196 NVA LMS 0.426357 0.739583
197 SA8 0.42623 0.696629
198 PAP 0.42623 0.829268
199 FNK 0.425926 0.826087
200 M24 0.425676 0.806818
201 YSA 0.425373 0.782609
202 53H 0.425197 0.726316
203 5CA 0.425197 0.782609
204 TSB 0.425197 0.76087
205 ITT 0.425 0.795181
206 A5A 0.424 0.75
207 AOC 0.422414 0.73494
208 BTX 0.42069 0.820225
209 SMM 0.420635 0.695652
210 GSU 0.419847 0.782609
211 SFD 0.41875 0.757576
212 NSS 0.418605 0.782609
213 52H 0.417323 0.726316
214 54H 0.417323 0.734043
215 VMS 0.417323 0.734043
216 JB6 0.416667 0.857143
217 6AD 0.416 0.837209
218 NDC 0.414013 0.804598
219 ODP 0.413793 0.858824
220 KXW 0.413043 0.715909
221 G5A 0.41129 0.763441
222 HFD 0.41129 0.802326
223 JSQ 0.41129 0.802326
224 RAB 0.411215 0.731707
225 ADN 0.411215 0.731707
226 XYA 0.411215 0.731707
227 AHZ 0.410072 0.797753
228 KAA 0.409091 0.739583
229 J4G 0.409091 0.86747
230 FDA 0.408805 0.833333
231 3AT 0.408 0.841463
232 0UM 0.407692 0.688889
233 ATP A A A 0.407407 0.829268
234 ATP A 0.407407 0.829268
235 LPA AMP 0.407143 0.797753
236 6FA 0.40625 0.8
237 AR6 AR6 0.405797 0.841463
238 PPS 0.404762 0.766667
239 7D5 0.403509 0.744186
240 AV2 0.401575 0.776471
241 K15 0.401515 0.673913
242 AMP DBH 0.40146 0.821429
243 WSA 0.401408 0.791209
244 AMP NAD 0.401361 0.853659
245 4TA 0.401361 0.872093
246 FAD 0.401235 0.808989
247 FAS 0.401235 0.808989
248 F2N 0.401163 0.835165
249 A3P 0.4 0.817073
250 AVV 0.4 0.804598
251 5CD 0.4 0.698795
252 A2P 0.4 0.804878
253 3DH 0.4 0.694118
Similar Ligands (3D)
Ligand no: 1; Ligand: 80F; Similar ligands found: 0
No: Ligand Similarity coefficient
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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