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: 232
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 NAX 0.571429 0.939024
10 6V0 0.571429 0.914634
11 TXD 0.571429 0.857143
12 BA3 0.570093 0.864198
13 TXE 0.566929 0.879518
14 AP5 0.564815 0.864198
15 B4P 0.564815 0.864198
16 ADP 0.564815 0.841463
17 ATP 0.563636 0.841463
18 HEJ 0.563636 0.841463
19 AN2 0.559633 0.831325
20 5FA 0.558559 0.841463
21 APR 0.558559 0.864198
22 AQP 0.558559 0.841463
23 AR6 0.558559 0.864198
24 SRP 0.556522 0.878049
25 5AL 0.552632 0.853659
26 A1R 0.550847 0.835294
27 AMO 0.550847 0.901235
28 ACP 0.54955 0.843373
29 0WD 0.548872 0.914634
30 A22 0.547009 0.853659
31 DG1 0.546763 0.914634
32 1DG 0.546763 0.914634
33 AT4 0.545455 0.855422
34 ANP 0.54386 0.821429
35 ACQ 0.54386 0.843373
36 M33 0.540541 0.831325
37 CA0 0.540541 0.865854
38 AD9 0.539823 0.821429
39 AGS 0.539823 0.845238
40 SAP 0.539823 0.845238
41 ADJ 0.537879 0.872093
42 NDP 0.537879 0.914634
43 ADQ 0.537815 0.865854
44 4AD 0.537815 0.890244
45 50T 0.535714 0.809524
46 ME8 0.532787 0.83908
47 YAP 0.532258 0.890244
48 PRX 0.530973 0.77907
49 6YZ 0.529915 0.843373
50 8QN 0.529412 0.853659
51 OAD 0.528926 0.865854
52 ADX 0.526786 0.786517
53 LAD 0.52459 0.837209
54 AMP 0.523364 0.817073
55 A 0.523364 0.817073
56 UP5 0.523077 0.890244
57 ATF 0.521368 0.811765
58 AHX 0.520661 0.847059
59 PTJ 0.520325 0.804598
60 NB8 0.520325 0.869048
61 3OD 0.520325 0.865854
62 FA5 0.52 0.901235
63 F2R 0.518519 0.820225
64 9X8 0.516393 0.86747
65 4TC 0.515152 0.891566
66 PAJ 0.512397 0.816092
67 A3R 0.512397 0.835294
68 WAQ 0.512195 0.835294
69 NXX 0.51145 0.878049
70 DND 0.51145 0.878049
71 00A 0.508197 0.835294
72 TXA 0.508065 0.855422
73 APC 0.504348 0.833333
74 OOB 0.504132 0.876543
75 25L 0.504 0.853659
76 48N 0.503817 0.847059
77 DQV 0.5 0.876543
78 TYM 0.496241 0.901235
79 OMR 0.496241 0.788889
80 B5M 0.496063 0.845238
81 BIS 0.496 0.793103
82 ABM 0.495495 0.797619
83 YLP 0.492424 0.8
84 XAH 0.492188 0.797753
85 25A 0.491803 0.841463
86 5SV 0.491803 0.744444
87 TAT 0.491525 0.855422
88 T99 0.491525 0.855422
89 TYR AMP 0.488372 0.86747
90 9SN 0.488189 0.825581
91 PR8 0.488 0.827586
92 AP2 0.486726 0.833333
93 A12 0.486726 0.833333
94 1ZZ 0.484127 0.777778
95 FYA 0.484127 0.853659
96 DLL 0.483871 0.876543
97 DAL AMP 0.483607 0.831325
98 5X8 0.482759 0.768293
99 YLA 0.481752 0.820225
100 YLB 0.481481 0.8
101 YLC 0.481481 0.83908
102 AFH 0.480916 0.837209
103 3UK 0.48 0.865854
104 9ZD 0.479675 0.813953
105 9ZA 0.479675 0.813953
106 AYB 0.478261 0.791209
107 CNA 0.478261 0.878049
108 NZQ 0.478261 0.926829
109 SRA 0.477477 0.821429
110 B5V 0.47619 0.855422
111 ADV 0.474576 0.855422
112 RBY 0.474576 0.855422
113 AU1 0.474138 0.821429
114 COD 0.471429 0.793478
115 NPW 0.471014 0.927711
116 139 0.471014 0.870588
117 T5A 0.471014 0.905882
118 7MD 0.469697 0.83908
119 NAQ 0.468966 0.804598
120 TXP 0.467626 0.847059
121 A4P 0.467153 0.842697
122 GAP 0.466667 0.821429
123 4UV 0.465649 0.91358
124 SON 0.465517 0.855422
125 ADP PO3 0.462185 0.817073
126 G3A 0.462121 0.825581
127 B5Y 0.461538 0.845238
128 NAD 0.460993 0.853659
129 NMN AMP PO4 0.460993 0.890244
130 UPA 0.459854 0.879518
131 G5P 0.458647 0.825581
132 ARG AMP 0.458647 0.788889
133 ADP BMA 0.456693 0.843373
134 GTA 0.455224 0.797753
135 A3D 0.454545 0.843373
136 IOT 0.453237 0.791209
137 LAQ 0.451852 0.818182
138 A2R 0.451613 0.853659
139 MAP 0.448 0.802326
140 4UU 0.447761 0.91358
141 NDE 0.447368 0.833333
142 ADP ALF 0.447154 0.761364
143 ALF ADP 0.447154 0.761364
144 N0B 0.445946 0.840909
145 SFG 0.445378 0.73494
146 NJP 0.443662 0.845238
147 VO4 ADP 0.443548 0.809524
148 ADP VO4 0.443548 0.809524
149 NAE 0.442177 0.823529
150 2A5 0.441667 0.8
151 FB0 0.441558 0.75
152 EEM 0.439024 0.681319
153 7MC 0.438849 0.820225
154 ATR 0.438017 0.817073
155 DZD 0.4375 0.837209
156 GA7 0.437037 0.833333
157 7D4 0.436975 0.767442
158 ZID 0.436242 0.843373
159 YLY 0.435374 0.791209
160 MYR AMP 0.435115 0.758242
161 62F 0.434783 0.797753
162 4UW 0.434783 0.880952
163 SAH 0.434426 0.75
164 SAI 0.434426 0.72093
165 NA7 0.434109 0.833333
166 TAD 0.433824 0.858824
167 5AS 0.432203 0.708333
168 SSA 0.432 0.782609
169 S7M 0.432 0.7
170 AF3 ADP 3PG 0.431655 0.795455
171 XNP 0.430556 0.892857
172 LMS 0.429825 0.747253
173 LSS 0.429688 0.747368
174 DSZ 0.429688 0.802198
175 BT5 0.427586 0.831461
176 7D3 0.42735 0.767442
177 NVA LMS 0.426357 0.739583
178 SA8 0.42623 0.696629
179 PAP 0.42623 0.829268
180 FNK 0.425926 0.826087
181 M24 0.425676 0.806818
182 YSA 0.425373 0.782609
183 TSB 0.425197 0.76087
184 53H 0.425197 0.726316
185 5CA 0.425197 0.782609
186 ITT 0.425 0.795181
187 A5A 0.424 0.75
188 LEU LMS 0.423077 0.739583
189 AOC 0.422414 0.73494
190 BTX 0.42069 0.820225
191 SMM 0.420635 0.695652
192 A A 0.419847 0.819277
193 GSU 0.419847 0.782609
194 SFD 0.41875 0.757576
195 NSS 0.418605 0.782609
196 54H 0.417323 0.734043
197 52H 0.417323 0.726316
198 VMS 0.417323 0.734043
199 JB6 0.416667 0.857143
200 6AD 0.416 0.837209
201 NDC 0.414013 0.804598
202 ODP 0.413793 0.858824
203 G5A 0.41129 0.763441
204 HFD 0.41129 0.802326
205 RAB 0.411215 0.731707
206 XYA 0.411215 0.731707
207 ADN 0.411215 0.731707
208 AHZ 0.410072 0.797753
209 KAA 0.409091 0.739583
210 FDA 0.408805 0.833333
211 3AT 0.408 0.841463
212 0UM 0.407692 0.688889
213 ATP A A A 0.407407 0.829268
214 LPA AMP 0.407143 0.797753
215 6FA 0.40625 0.8
216 AR6 AR6 0.405797 0.841463
217 PPS 0.404762 0.766667
218 7D5 0.403509 0.744186
219 AV2 0.401575 0.776471
220 K15 0.401515 0.673913
221 AMP DBH 0.40146 0.821429
222 WSA 0.401408 0.791209
223 AMP NAD 0.401361 0.853659
224 4TA 0.401361 0.872093
225 FAS 0.401235 0.808989
226 FAD 0.401235 0.808989
227 F2N 0.401163 0.835165
228 A3P 0.4 0.817073
229 5CD 0.4 0.698795
230 AVV 0.4 0.804598
231 3DH 0.4 0.694118
232 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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