Structure of PDB 4xb1 Chain B Binding Site BS01

Receptor Information
>4xb1 Chain B (length=319) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVNISIFGFGTVGRALAEIIAEKSRIFGVELNVISITDRSGTIWGDFDL
LEAKEVKESTGKLSNIGDYEVYNFSPQELVEEVKPNILVDVSSWDEAHEM
YKVALGEGISVVTSNKPPIANYYDELMNLAKENNAGIFFESTVMAGTPII
GVLRENLLGENIKRIDAVVNASTTFILTKMSEGKTLDDAIEEAKSLGILE
EDPSKDIDGIDAYYKAKILHWVSYGEPPEEEERLGIREVRDARNVRLVAQ
VSKGKISVKPRKLSSDNPLLVEGVQNAAVIRTNNLGEVILKGPGGGGRVT
ASGVFTDIIKATLKFPNLR
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
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)OP(=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[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
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)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain4xb1 Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4xb1 Crystal Structures of a Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest a Novel Cofactor Binding Mode for Oxidoreductases.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F8 F10 G11 T12 V13 D39 R40 K57 V91 S92 S93 S114 K116 S141 G295 T300
Binding residue
(residue number reindexed from 1)		F8 F10 G11 T12 V13 D39 R40 K57 V91 S92 S93 S114 K116 S141 G295 T300
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D211 K215
Catalytic site (residue number reindexed from 1) D211 K215
Enzyme Commision number 1.1.1.3: homoserine dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004412 homoserine dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050661 NADP binding
GO:0070403 NAD+ binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0009086 methionine biosynthetic process
GO:0009088 threonine biosynthetic process
GO:0009090 homoserine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4xb1, PDBe:4xb1, PDBj:4xb1
PDBsum4xb1
PubMed26154028
UniProtO58802|DHOM_PYRHO Homoserine dehydrogenase (Gene Name=PH1075)

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