Structure of PDB 1bd0 Chain A Binding Site BS01

Receptor Information
>1bd0 Chain A (length=381) 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
INYEVPCTISYRVPRIFFRHKRIMEVRNAIG
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
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]
PDB1bd0 Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		K39 Y43 R136 H166 N203 S204 R219 G221 I222 Y354
Binding residue
(residue number reindexed from 1)		K38 Y42 R135 H165 N202 S203 R218 G220 I221 Y353
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

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

[Back to BioLiP]