-->
Receptor
PDB id Resolution Class Description Source Keywords
4AJS 1.8 Å EC: 1.1.1.42 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTAN COMPLEX WITH ISOCITRATE, MAGNESIUM(II), ADENOSINE 2',5'-BIPA ND RIBOSYLNICOTINAMIDE-5'-PHOSPHATE ESCHERICHIA COLI OXIDOREDUCTASE OXIDATIVE BETA-DECARBOXYLATION
Ref.: INDUCED FIT AND THE CATALYTIC MECHANISM OF ISOCITRA DEHYDROGENASE. BIOCHEMISTRY V. 51 7098 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A2P A:501;
Valid;
none;
submit data
427.201 C10 H15 N5 O10 P2 c1nc(...
ICT A:502;
Valid;
none;
submit data
192.124 C6 H8 O7 C([C@...
MG A:503;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
NMN A:504;
Valid;
none;
submit data
335.227 C11 H16 N2 O8 P c1cc(...
SO4 A:505;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1GRO 2.5 Å EC: 1.1.1.42 REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOC DEHYDROGENASE: MULTIPLE ROLES FOR N115 ESCHERICHIA COLI OXIDOREDUCTASE NADP PHOSPHORYLATION GLYOXYLATE BYPASS OXIDOREDUCTASE (NAD(A)-CHOH(D))
Ref.: SECOND-SITE SUPPRESSION OF REGULATORY PHOSPHORYLATI ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE. PROTEIN SCI. V. 5 287 1996
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1PB1 - ICT C6 H8 O7 C([C@@H]([....
2 5ICD - ICT C6 H8 O7 C([C@@H]([....
3 1P8F - ICT C6 H8 O7 C([C@@H]([....
4 4AJB - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
5 1CW4 - AKG C5 H6 O5 C(CC(=O)O)....
6 4AJC - AKG C5 H6 O5 C(CC(=O)O)....
7 4AJS - ICT C6 H8 O7 C([C@@H]([....
8 1BL5 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 1GRP Ki = 0.189 mM ICT C6 H8 O7 C([C@@H]([....
10 9ICD Kd = 125 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
11 4AJ3 - ICT C6 H8 O7 C([C@@H]([....
12 4AJA - ICT C6 H8 O7 C([C@@H]([....
13 1AI3 Ki = 403 uM NDO C21 H27 N6 O18 P3 c1cc(c[n+]....
14 1ISO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 4BNP Ki = 96 uM ICT C6 H8 O7 C([C@@H]([....
16 1CW1 - ICT C6 H8 O7 C([C@@H]([....
17 1GRO Ki = 0.033 uM ICT C6 H8 O7 C([C@@H]([....
18 1IDE - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1HJ6 - IPM C7 H12 O5 CC(C)[C@@H....
20 1AI2 Ki = 2.7 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
21 8ICD - ICT C6 H8 O7 C([C@@H]([....
70% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1PB1 - ICT C6 H8 O7 C([C@@H]([....
2 5ICD - ICT C6 H8 O7 C([C@@H]([....
3 1P8F - ICT C6 H8 O7 C([C@@H]([....
4 4AJB - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
5 1CW4 - AKG C5 H6 O5 C(CC(=O)O)....
6 4AJC - AKG C5 H6 O5 C(CC(=O)O)....
7 4AJS - ICT C6 H8 O7 C([C@@H]([....
8 1BL5 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 1GRP Ki = 0.189 mM ICT C6 H8 O7 C([C@@H]([....
10 9ICD Kd = 125 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
11 4AJ3 - ICT C6 H8 O7 C([C@@H]([....
12 4AJA - ICT C6 H8 O7 C([C@@H]([....
13 1AI3 Ki = 403 uM NDO C21 H27 N6 O18 P3 c1cc(c[n+]....
14 1ISO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 4BNP Ki = 96 uM ICT C6 H8 O7 C([C@@H]([....
16 1CW1 - ICT C6 H8 O7 C([C@@H]([....
17 1GRO Ki = 0.033 uM ICT C6 H8 O7 C([C@@H]([....
18 1IDE - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1HJ6 - IPM C7 H12 O5 CC(C)[C@@H....
20 1AI2 Ki = 2.7 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
21 8ICD - ICT C6 H8 O7 C([C@@H]([....
22 1HQS - CIT C6 H8 O7 C(C(=O)O)C....
23 2D4V - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PB1 - ICT C6 H8 O7 C([C@@H]([....
2 5ICD - ICT C6 H8 O7 C([C@@H]([....
3 1P8F - ICT C6 H8 O7 C([C@@H]([....
4 4AJB - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
5 1CW4 - AKG C5 H6 O5 C(CC(=O)O)....
6 4AJC - AKG C5 H6 O5 C(CC(=O)O)....
7 4AJS - ICT C6 H8 O7 C([C@@H]([....
8 1BL5 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
9 1GRP Ki = 0.189 mM ICT C6 H8 O7 C([C@@H]([....
10 9ICD Kd = 125 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
11 4AJ3 - ICT C6 H8 O7 C([C@@H]([....
12 4AJA - ICT C6 H8 O7 C([C@@H]([....
13 1AI3 Ki = 403 uM NDO C21 H27 N6 O18 P3 c1cc(c[n+]....
14 1ISO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 4BNP Ki = 96 uM ICT C6 H8 O7 C([C@@H]([....
16 1CW1 - ICT C6 H8 O7 C([C@@H]([....
17 1GRO Ki = 0.033 uM ICT C6 H8 O7 C([C@@H]([....
18 1IDE - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
19 1HJ6 - IPM C7 H12 O5 CC(C)[C@@H....
20 1AI2 Ki = 2.7 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
21 8ICD - ICT C6 H8 O7 C([C@@H]([....
22 1HQS - CIT C6 H8 O7 C(C(=O)O)C....
23 2D4V - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 1XKD - ICT C6 H8 O7 C([C@@H]([....
25 1TYO - ENP C17 H24 N5 O17 P3 c1cn2cnc3c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A2P; Similar ligands found: 285
No: Ligand ECFP6 Tc MDL keys Tc
1 A2P 1 1
2 ATR 0.835616 0.985294
3 2AM 0.80597 0.956522
4 A2R 0.772152 0.943662
5 A22 0.7625 0.943662
6 25A 0.731707 0.957143
7 NA7 0.72619 0.917808
8 V3L 0.7 0.957143
9 AMP 0.684932 0.956522
10 A 0.684932 0.956522
11 A3P 0.684211 0.985294
12 OVE 0.675676 0.916667
13 7D5 0.643836 0.888889
14 3AM 0.626667 0.942029
15 25L 0.626374 0.943662
16 PO4 PO4 A A A A PO4 0.611111 0.942029
17 NPW 0.598039 0.848101
18 NDP 0.598039 0.881579
19 XNP 0.596154 0.858974
20 PAP 0.595238 0.971014
21 TXP 0.592233 0.881579
22 NZQ 0.592233 0.87013
23 NJP 0.586538 0.905405
24 ODP 0.586538 0.87013
25 ABM 0.575 0.902778
26 A2D 0.575 0.929577
27 PPS 0.574713 0.858974
28 ADP 0.573171 0.957143
29 SRA 0.56962 0.90411
30 AN2 0.566265 0.943662
31 2A5 0.564706 0.90411
32 AP2 0.560976 0.917808
33 A12 0.560976 0.917808
34 BA3 0.560976 0.929577
35 AGS 0.55814 0.905405
36 SAP 0.55814 0.905405
37 B4P 0.554217 0.929577
38 AP5 0.554217 0.929577
39 HEJ 0.552941 0.957143
40 ATP 0.552941 0.957143
41 7D3 0.548781 0.890411
42 AT4 0.547619 0.917808
43 5FA 0.546512 0.957143
44 APC 0.546512 0.917808
45 AQP 0.546512 0.957143
46 ADN 0.541667 0.802817
47 RAB 0.541667 0.802817
48 XYA 0.541667 0.802817
49 CA0 0.541176 0.90411
50 7D4 0.541176 0.890411
51 M33 0.541176 0.916667
52 AU1 0.541176 0.930556
53 ADX 0.541176 0.835443
54 NAP 0.539823 0.930556
55 DG1 0.535088 0.881579
56 TAP 0.535088 0.893333
57 1DG 0.535088 0.881579
58 ACP 0.534884 0.930556
59 50T 0.534884 0.916667
60 NA0 0.530435 0.917808
61 7L1 0.530435 0.761364
62 APR 0.528736 0.929577
63 AR6 0.528736 0.929577
64 PRX 0.528736 0.878378
65 T99 0.52809 0.917808
66 ACQ 0.52809 0.930556
67 TAT 0.52809 0.917808
68 DA 0.52439 0.915493
69 D5M 0.52439 0.915493
70 ADV 0.522727 0.891892
71 RBY 0.522727 0.891892
72 AD9 0.522727 0.930556
73 ADQ 0.521277 0.90411
74 LMS 0.518519 0.8125
75 SON 0.511628 0.917808
76 ANP 0.511111 0.930556
77 6YZ 0.51087 0.930556
78 NMN AMP PO4 0.509091 0.855263
79 7D7 0.506849 0.75
80 ADP PO3 0.505618 0.928571
81 5AL 0.505495 0.916667
82 ATF 0.5 0.917808
83 AV2 0.5 0.929577
84 CO7 0.495935 0.770115
85 AR6 AR6 0.495146 0.902778
86 OAD 0.494845 0.90411
87 9X8 0.494845 0.88
88 ENP 0.494845 0.878378
89 ADP BMA 0.494845 0.878378
90 5SV 0.494737 0.833333
91 SRP 0.494624 0.891892
92 GAP 0.494505 0.878378
93 101 0.493976 0.888889
94 5N5 0.486842 0.777778
95 BIS 0.484848 0.893333
96 PTJ 0.484848 0.881579
97 00A 0.484536 0.868421
98 MAP 0.484211 0.905405
99 ADP ALF 0.483871 0.855263
100 ALF ADP 0.483871 0.855263
101 5AS 0.482759 0.764706
102 N01 0.482456 0.890411
103 5CD 0.480519 0.788732
104 A4D 0.480519 0.777778
105 9ZD 0.479167 0.893333
106 OOB 0.479167 0.916667
107 9ZA 0.479167 0.893333
108 8QN 0.479167 0.916667
109 ADP VO4 0.478723 0.916667
110 VO4 ADP 0.478723 0.916667
111 3AT 0.478261 0.957143
112 DTA 0.475 0.77027
113 A A 0.474747 0.929577
114 4AD 0.474227 0.88
115 A1R 0.474227 0.868421
116 PAJ 0.474227 0.846154
117 AMO 0.474227 0.891892
118 A3R 0.474227 0.868421
119 A3G 0.470588 0.76
120 AOC 0.470588 0.805556
121 1ZZ 0.47 0.825
122 3OD 0.47 0.90411
123 FYA 0.47 0.890411
124 AHX 0.469388 0.857143
125 DLL 0.469388 0.916667
126 MTA 0.469136 0.756757
127 0WD 0.469027 0.881579
128 DAL AMP 0.46875 0.890411
129 UPA 0.46789 0.868421
130 2VA 0.466667 0.76
131 5X8 0.466667 0.746667
132 DAT 0.466667 0.916667
133 TM1 0.465347 0.802469
134 A A A 0.464646 0.890411
135 3UK 0.464646 0.90411
136 APU 0.463636 0.905405
137 EP4 0.4625 0.736842
138 DTP 0.462366 0.916667
139 9SN 0.460784 0.857143
140 WAQ 0.46 0.868421
141 LAD 0.46 0.846154
142 B5V 0.46 0.891892
143 PR8 0.46 0.835443
144 6RE 0.458824 0.74359
145 3DH 0.457831 0.756757
146 M2T 0.45679 0.717949
147 NVA 2AD 0.456522 0.721519
148 ATP A A A 0.456311 0.915493
149 ME8 0.455446 0.825
150 JB6 0.455446 0.868421
151 NB8 0.455446 0.857143
152 TXA 0.455446 0.891892
153 GGZ 0.453608 0.833333
154 5AD 0.453333 0.753623
155 ANZ 0.45283 0.831169
156 G5A 0.451613 0.764706
157 SO8 0.451613 0.75
158 VRT 0.451613 0.730769
159 MYR AMP 0.45098 0.802469
160 PUA 0.449153 0.87013
161 Y3J 0.448718 0.732394
162 IMO 0.448276 0.914286
163 AS 0.448276 0.866667
164 QQY 0.447059 0.849315
165 103 0.447059 0.847222
166 ACK 0.447059 0.898551
167 OMR 0.445455 0.814815
168 A3S 0.444444 0.77027
169 3AD 0.443038 0.814286
170 FA5 0.442308 0.891892
171 YAP 0.442308 0.88
172 B5Y 0.442308 0.88
173 B5M 0.442308 0.88
174 AFH 0.439252 0.846154
175 TSB 0.438776 0.783133
176 XAH 0.438095 0.825
177 A5A 0.4375 0.792683
178 A U 0.4375 0.855263
179 DSH 0.436782 0.708861
180 NAX 0.436364 0.835443
181 NAI 0.436364 0.868421
182 QQX 0.435294 0.837838
183 A3T 0.434783 0.780822
184 4UV 0.433962 0.88
185 TYR AMP 0.433962 0.855263
186 SSA 0.43299 0.764706
187 J7C 0.431818 0.753247
188 DDS 0.431579 0.888889
189 LAQ 0.431193 0.825
190 ZAS 0.430233 0.75
191 G3A 0.429907 0.881579
192 52H 0.428571 0.764706
193 ETB 0.428571 0.797619
194 AP0 0.428571 0.857143
195 CC5 0.428571 0.8
196 VMS 0.428571 0.77381
197 54H 0.428571 0.77381
198 DCA 0.428571 0.788235
199 48N 0.427273 0.857143
200 S4M 0.426966 0.651163
201 8BR 0.426966 0.891892
202 7MD 0.425926 0.825
203 G5P 0.425926 0.881579
204 ARG AMP 0.425926 0.814815
205 GA7 0.425926 0.866667
206 4UU 0.425926 0.88
207 3L1 0.425 0.756757
208 3D1 0.425 0.756757
209 5CA 0.424242 0.764706
210 8X1 0.424242 0.738636
211 53H 0.424242 0.764706
212 6V0 0.423423 0.857143
213 4UW 0.423423 0.846154
214 TXD 0.423423 0.868421
215 UP5 0.423423 0.88
216 PAX 0.422764 0.8375
217 MAO 0.422222 0.743902
218 71V 0.422222 0.868421
219 DQV 0.422018 0.916667
220 TAD 0.422018 0.846154
221 GTA 0.422018 0.848101
222 COA 0.421488 0.788235
223 0T1 0.421488 0.788235
224 SAH 0.421053 0.727273
225 AMP DBH 0.420561 0.853333
226 NEC 0.420455 0.72973
227 TYM 0.419643 0.891892
228 TXE 0.419643 0.868421
229 SFG 0.419355 0.733333
230 NDO 0.418033 0.90411
231 P5A 0.417476 0.730337
232 139 0.417391 0.835443
233 4TC 0.415929 0.857143
234 DSZ 0.415842 0.764706
235 NSS 0.415842 0.764706
236 LSS 0.415842 0.747126
237 A3N 0.41573 0.746667
238 AAM 0.41573 0.956522
239 WMP 0.415254 0.876712
240 LPA AMP 0.414414 0.802469
241 YLP 0.414414 0.804878
242 ZZB 0.413793 0.802469
243 A7D 0.413043 0.76
244 C2R 0.411765 0.863014
245 AMZ 0.411765 0.875
246 NVA LMS 0.411765 0.738636
247 CAO 0.41129 0.761364
248 COS 0.41129 0.770115
249 30N 0.41129 0.72043
250 AMX 0.41129 0.797619
251 GJV 0.411111 0.734177
252 NXX 0.410714 0.891892
253 DND 0.410714 0.891892
254 128 0.410714 0.783133
255 SA8 0.410526 0.691358
256 A5D 0.410526 0.77027
257 PGS 0.408602 0.844156
258 A C A C 0.408333 0.833333
259 2SA 0.408163 0.891892
260 SCO 0.408 0.788235
261 CMX 0.408 0.788235
262 LEU LMS 0.407767 0.738636
263 G A A A 0.40678 0.857143
264 SAI 0.40625 0.717949
265 6C6 0.40625 0.866667
266 CA6 0.40625 0.697917
267 12D 0.405405 0.792683
268 AHZ 0.405405 0.802469
269 ADJ 0.405172 0.814815
270 FCX 0.404762 0.761364
271 ACO 0.404762 0.761364
272 FAM 0.404762 0.770115
273 S7M 0.40404 0.674699
274 GSU 0.403846 0.764706
275 KAA 0.403846 0.738636
276 YLC 0.403509 0.825
277 7MC 0.403509 0.804878
278 YLB 0.403509 0.804878
279 NIA 0.402299 0.807692
280 2GP 0.402174 0.891892
281 6IA 0.402062 0.822785
282 HAX 0.401575 0.770115
283 9K8 0.4 0.7
284 A4P 0.4 0.807229
285 80F 0.4 0.804878
Ligand no: 2; Ligand: ICT; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 ICT 1 1
2 DMR 0.444444 0.904762
3 LMR 0.444444 0.904762
4 MLT 0.444444 0.904762
5 3HG 0.423077 0.772727
6 TLA 0.416667 0.727273
7 SRT 0.416667 0.727273
8 TAR 0.416667 0.727273
9 3HR 0.407407 0.608696
10 3HL 0.407407 0.608696
Ligand no: 3; Ligand: NMN; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 NMN 1 1
2 NNR 0.693548 0.818182
3 NCN 0.647887 0.892308
4 8ID 0.524752 0.807692
5 NGD 0.514563 0.831169
6 NHD 0.509434 0.875
7 NAD 0.509434 0.875
8 NAJ 0.504762 0.875
9 NDO 0.491071 0.888889
10 NAP 0.486726 0.888889
11 NFD 0.486239 0.828947
12 NBP 0.465517 0.831169
13 DND 0.461538 0.851351
14 NXX 0.461538 0.851351
15 A3D 0.421053 0.863014
16 N01 0.417391 0.849315
17 AMP NAD 0.415929 0.849315
18 CH 0.407407 0.849315
19 NA0 0.404959 0.876712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1GRO; Ligand: ICT; Similar sites found with APoc: 35
This union binding pocket(no: 1) in the query (biounit: 1gro.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 4UYW H1S 1.30548
2 3B2Q AES 1.68269
3 1PCA CIT 2.23325
4 1IZC PYR 2.35988
5 4RF7 ARG 2.40385
6 4C2C ALA ALA ALA 2.40385
7 3QDX CBS 2.7972
8 3QDW NDG 2.7972
9 3QDV NDG 2.7972
10 4BHL ARG 3.37079
11 5O5Y GLC 3.60577
12 4OWK NGA 3.62319
13 4EHQ GBL 4.05405
14 5OCQ CIT 4.5614
15 2D24 XYS XYS 4.80769
16 2II3 CAO 4.96183
17 2XG5 EC5 5.04587
18 2XG5 EC2 5.04587
19 1NME 159 5.47945
20 3A23 GAL 5.52885
21 2Z4T C5P 5.76923
22 4C2W ANP 6.09319
23 1KNM LAT 6.15385
24 2ZQO NGA 7.69231
25 2UXR ICT 8.45771
26 5E5U MLT 9.4697
27 5A04 BGC 11.7994
28 1PVC ILE SER GLU VAL 14.7059
29 1RL4 BL5 20.2128
30 1A05 IPM 42.7374
31 5J32 IPM 42.928
32 5HN6 IPM 43.0595
33 1HEX NAD 44.3478
34 3FLK OXL 44.5055
35 4Y1P IPM 45.1039
Pocket No.: 2; Query (leader) PDB : 1GRO; Ligand: ICT; 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: 1gro.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback