Structure of PDB 1bd0 Chain B Binding Site BS01

Receptor Information
>1bd0 Chain B (length=380) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVA
RTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRI
ALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVAL
IERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHC
ANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRL
VHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDG
QKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLET
INYEVPCTISYRVPRIFFRHKRIMEVRNAI
Ligand information
Ligand IDIN5
InChIInChI=1S/C10H18N2O8P2/c1-6-10(13)9(4-12-7(2)21(14,15)16)8(3-11-6)5-20-22(17,18)19/h3,7,12-13H,4-5H2,1-2H3,(H2,14,15,16)(H2,17,18,19)/t7-/m1/s1
InChIKeyWHDCJKAOZPBUAY-SSDOTTSWSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)[P](O)(O)=O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)P(=O)(O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)P(=O)(O)O)O
CACTVS 3.341C[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNC(C)P(=O)(O)O)C
FormulaC10 H18 N2 O8 P2
Name{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID
ChEMBL
DrugBankDB03327
ZINCZINC000002047885
PDB chain1bd0 Chain A Residue 389 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1bd0 Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y265 C311 M312
Binding residue
(residue number reindexed from 1)		Y264 C310 M311
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K39 R136 H166 R219 Y265 C311 D313
Catalytic site (residue number reindexed from 1) K38 R135 H165 R218 Y264 C310 D312
Enzyme Commision number 5.1.1.1: alanine racemase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008784 alanine racemase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006522 alanine metabolic process
GO:0009252 peptidoglycan biosynthetic process
GO:0030632 D-alanine biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1bd0, PDBe:1bd0, PDBj:1bd0
PDBsum1bd0
PubMed9671513
UniProtP10724|ALR_GEOSE Alanine racemase (Gene Name=alr)

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