Receptor
PDB id Resolution Class Description Source Keywords
1XKD 2.3 Å EC: 1.1.1.42 TERNARY COMPLEX OF ISOCITRATE DEHYDROGENASE FROM THE HYPERTH AEROPYRUM PERNIX AEROPYRUM PERNIX ENZYME TERNARY COMPLEX ISOCITRATE CA2+ NADP+ OXIDOREDUC
Ref.: ISOCITRATE DEHYDROGENASE FROM THE HYPERTHERMOPHILE PERNIX: X-RAY STRUCTURE ANALYSIS OF A TERNARY ENZYME-SUBSTRATE COMPLEX AND THERMAL STABILITY. J.MOL.BIOL. V. 345 559 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1005;
A:1006;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
ICT A:1002;
B:1004;
Valid;
Valid;
none;
none;
submit data
192.124 C6 H8 O7 C([C@...
NAP A:1001;
B:1003;
Valid;
Valid;
none;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1XKD 2.3 Å EC: 1.1.1.42 TERNARY COMPLEX OF ISOCITRATE DEHYDROGENASE FROM THE HYPERTH AEROPYRUM PERNIX AEROPYRUM PERNIX ENZYME TERNARY COMPLEX ISOCITRATE CA2+ NADP+ OXIDOREDUC
Ref.: ISOCITRATE DEHYDROGENASE FROM THE HYPERTHERMOPHILE PERNIX: X-RAY STRUCTURE ANALYSIS OF A TERNARY ENZYME-SUBSTRATE COMPLEX AND THERMAL STABILITY. J.MOL.BIOL. V. 345 559 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1XKD - ICT C6 H8 O7 C([C@@H]([....
2 1TYO - ENP C17 H24 N5 O17 P3 c1cn2cnc3c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1XKD - ICT C6 H8 O7 C([C@@H]([....
2 1TYO - ENP C17 H24 N5 O17 P3 c1cn2cnc3c....
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: ICT; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 ICT 1 1
2 LMR 0.444444 0.904762
3 DMR 0.444444 0.904762
4 MLT 0.444444 0.904762
5 3HG 0.423077 0.772727
6 TAR 0.416667 0.727273
7 TLA 0.416667 0.727273
8 SRT 0.416667 0.727273
9 3HR 0.407407 0.608696
10 3HL 0.407407 0.608696
Ligand no: 2; Ligand: NAP; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XKD; Ligand: ICT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1xkd.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1XKD; Ligand: NAP; 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: 1xkd.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1XKD; Ligand: NAP; Similar sites found: 22
This union binding pocket(no: 3) in the query (biounit: 1xkd.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WBD CIT 0.039 0.40628 1.6092
2 4C2W ANP 0.005323 0.45183 1.79211
3 5FJJ MAN 0.01549 0.423 1.83908
4 1YQT ADP 0.02792 0.41163 2.29885
5 3W9F I3P 0.02633 0.42746 3.07692
6 2Z49 AMG 0.02046 0.40699 3.24074
7 2G50 PYR 0.03612 0.40264 3.44828
8 1O5O U5P 0.01314 0.4146 3.61991
9 2XT3 ADP 0.03823 0.40532 3.77907
10 2QES ADE 0.04564 0.40103 3.83142
11 1UCD U5P 0.009005 0.43998 4.21053
12 1UNQ 4IP 0.04353 0.40064 4.8
13 4TR9 ASP TRP ASN 0.01642 0.40621 5.14905
14 4N14 WR7 0.02156 0.41657 5.41401
15 2AF6 BRU 0.03862 0.40372 5.42636
16 1JPA ANP 0.03247 0.40783 6.08974
17 3KU0 ADE 0.03312 0.40824 6.3745
18 3KO0 TFP 0.03725 0.40288 6.93069
19 4K7O EKZ 0.02871 0.40928 11.3095
20 2UXR ICT 0.02647 0.41113 15.6716
21 3IWD M2T 0.035 0.40464 36.7647
22 1HEX NAD 0.00000002352 0.60124 48.6957
Pocket No.: 4; Query (leader) PDB : 1XKD; Ligand: ICT; Similar sites found: 10
This union binding pocket(no: 4) in the query (biounit: 1xkd.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PCA CIT 0.01624 0.40706 2.48139
2 3W5N RAM 0.01315 0.40522 2.98851
3 1U25 IHS 0.009319 0.40841 3.2641
4 1YMT DR9 0.0268 0.40675 4.06504
5 1DL2 NAG 0.009443 0.42621 4.82759
6 3W68 4PT 0.01826 0.4045 5.6391
7 2UXR ICT 0.000000006202 0.71087 15.6716
8 5J32 IPM 0.000000003836 0.73101 43.1762
9 3FLK OXL 0.00000001153 0.72792 44.5055
10 1A05 IPM 0.000000006787 0.71842 46.648
Feedback