Structure of PDB 8hp3 Chain B Binding Site BS01

Receptor Information
>8hp3 Chain B (length=298) Species: 386414 (Hoylesella timonensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKIRAAIVGYGNIGKFTVEAVEAAEDFELVGIVRRQGAENKPAELAPYKV
VQDIKELEGVDVAILATPSRSCKEYAEKILPLGINTVDSFDIHTDIVDYR
SALMPLCKEHHAVSIISAGWDPGSDSVVRTLMQSLAPKGLSYTNFGPGMS
MGHSVCARSKKGVKNALSMTIPLGEGIHRRMVYVELEEGATLDEVTKEIK
ADPYFAHDETHVMAVDSVDAVKDMGHGVHLVRKGVSGKTQNQRMEFSMSI
NNPALTAQVLVNVARASMHQQPGCYTMVEIPVIDLLAGEREDLIKALV
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 chain8hp3 Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8hp3 Rational design of meso-diaminopimelate dehydrogenase to enhance reductive amination activity for efficient production of D-HPG
Resolution3.07 Å
Binding residue
(original residue number in PDB)		G10 Y11 G12 N13 I14 R35 R36 A67 T68 P69 S70 Y76 S90 D92 D122 N253
Binding residue
(residue number reindexed from 1)		G9 Y10 G11 N12 I13 R34 R35 A66 T67 P68 S69 Y75 S89 D91 D121 N252
Annotation score4
Enzymatic activity
Enzyme Commision number 1.4.1.16: diaminopimelate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0047850 diaminopimelate dehydrogenase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8hp3, PDBe:8hp3, PDBj:8hp3
PDBsum8hp3
PubMed37070978
UniProtA0A2K0XCZ3

[Back to BioLiP]