Structure of PDB 4yb4 Chain A Binding Site BS03

Receptor Information
>4yb4 Chain A (length=333) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AYRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSV
PEETVEKILSCHATLFGAATSPTRKVPGFFGAIRYLRRRLDLYANVRPAK
SRPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIADAVISKKASERIG
RAALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDI
IVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGD
TTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAKRVEKAV
DLVLERGPRTPDLGGDATTEAFTEAVVEALKSL
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain4yb4 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yb4 Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I202 N205
Binding residue
(residue number reindexed from 1)		I201 N204
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y125 K171 D204 D228 D232
Catalytic site (residue number reindexed from 1) Y124 K170 D203 D227 D231
Enzyme Commision number 1.1.1.286: isocitrate--homoisocitrate dehydrogenase.
Gene Ontology
Molecular Function
GO:0004449 isocitrate dehydrogenase (NAD+) activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047046 homoisocitrate dehydrogenase activity
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
GO:0009085 lysine biosynthetic process
GO:0019878 lysine biosynthetic process via aminoadipic acid

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4yb4, PDBe:4yb4, PDBj:4yb4
PDBsum4yb4
PubMed
UniProtQ72IW9|HICDH_THET2 Isocitrate/homoisocitrate dehydrogenase (Gene Name=hicd)

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