Receptor
PDB id Resolution Class Description Source Keywords
2QFY 2.1 Å EC: 1.1.1.42 CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVESIAE MITOCHONDRIAL DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH A-KETOGL SACCHAROMYCES CEREVISIAE ROSSMANN FOLD OXIDOREDUCTASE
Ref.: STRUCTURAL STUDIES OF SACCHAROMYCES CEREVESIAE MITO NADP-DEPENDENT ISOCITRATE DEHYDROGENASE IN DIFFEREN ENZYMATIC STATES REVEAL SUBSTANTIAL CONFORMATIONAL DURING THE CATALYTIC REACTION PROTEIN SCI. V. 17 1542 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:2001;
B:2002;
C:2003;
D:2004;
E:2005;
F:2006;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
146.098 C5 H6 O5 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2QFY 2.1 Å EC: 1.1.1.42 CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVESIAE MITOCHONDRIAL DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH A-KETOGL SACCHAROMYCES CEREVISIAE ROSSMANN FOLD OXIDOREDUCTASE
Ref.: STRUCTURAL STUDIES OF SACCHAROMYCES CEREVESIAE MITO NADP-DEPENDENT ISOCITRATE DEHYDROGENASE IN DIFFEREN ENZYMATIC STATES REVEAL SUBSTANTIAL CONFORMATIONAL DURING THE CATALYTIC REACTION PROTEIN SCI. V. 17 1542 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
2 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3INM - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5SUN ic50 = 0.59 uM 70Q C24 H22 N4 O4 S CN(C)S(=O)....
3 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
6 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
7 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
8 1T0L - ICT C6 H8 O7 C([C@@H]([....
9 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
11 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
12 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
13 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 4HCX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
15 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
16 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
17 1LWD - ICT C6 H8 O7 C([C@@H]([....
18 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
19 5H3E - ICT C6 H8 O7 C([C@@H]([....
20 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
21 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3INM - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5SUN ic50 = 0.59 uM 70Q C24 H22 N4 O4 S CN(C)S(=O)....
3 4L06 Kd = 0.12 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 4UMY - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 5DE1 ic50 = 46 nM 59D C28 H28 F N5 O3 C[C@@H]1CN....
6 5TQH ic50 = 0.02 uM 7J2 C23 H25 F N6 O2 Cc1cc(ccc1....
7 4UMX ic50 = 0.011 uM VVS C22 H30 N4 O CC(C)(C)CC....
8 1T0L - ICT C6 H8 O7 C([C@@H]([....
9 4L03 Kd = 0.013 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 5SVF ic50 = 0.22 uM 70P C18 H22 N4 O2 C[C@@H](c1....
11 4KZO Kd = 0.043 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
12 2QFY - AKG C5 H6 O5 C(CC(=O)O)....
13 2QFV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 4HCX - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
15 5SVN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
16 4JA8 - 1K9 C21 H18 F3 N3 O3 S2 c1cc(cc(c1....
17 1LWD - ICT C6 H8 O7 C([C@@H]([....
18 5I95 - AKG C5 H6 O5 C(CC(=O)O)....
19 5H3E - ICT C6 H8 O7 C([C@@H]([....
20 5I96 ic50 = 100 nM 69Q C19 H17 F6 N7 O CC(C)(CNc1....
21 5SVO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
22 2UXR - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 OOG 0.5 0.947368
3 69O 0.458333 0.714286
4 2IT 0.423077 0.615385
5 SHF 0.416667 0.666667
6 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2QFY; Ligand: AKG; 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: 2qfy.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2QFY; Ligand: AKG; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 2qfy.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YQC GLV 0.04005 0.40633 5.88235
2 2GUC MAN 0.01416 0.40365 7.37705
3 1HEX NAD 0.00001603 0.49634 11.8841
4 2D4V NAD 0.000003035 0.52259 12.6464
5 1WZ1 DNS 0.03547 0.40495 17.6991
6 5GRF ADP 0.003595 0.40268 23.5988
Pocket No.: 3; Query (leader) PDB : 2QFY; Ligand: AKG; Similar sites found: 9
This union binding pocket(no: 3) in the query (biounit: 2qfy.bio3) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4R74 F6P 0.0171 0.42482 3.11526
2 1P72 ADP 0.0452 0.41077 4.79042
3 5UL5 PLM 0.04791 0.41073 5.62061
4 5UL5 8D7 0.04791 0.41073 5.62061
5 4RSE PLM 0.02692 0.40799 5.62061
6 4IID NOJ 0.008166 0.4087 10.5386
7 2D4V FLC 0.00003434 0.47653 12.6464
8 1LEK GLU GLN TYR LYS PHE TYR SER VAL 0.02294 0.41162 14.1414
9 1A05 IPM 0.00006536 0.48277 26.5363
Pocket No.: 4; Query (leader) PDB : 2QFY; Ligand: AKG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2qfy.bio3) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2QFY; Ligand: AKG; Similar sites found: 2
This union binding pocket(no: 5) in the query (biounit: 2qfy.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Z9I GLY ALA THR VAL 0.03238 0.40426 2.46914
2 2YLN CYS 0.04206 0.40308 2.4735
Pocket No.: 6; Query (leader) PDB : 2QFY; Ligand: AKG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2qfy.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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