Structure of PDB 3k5x Chain A Binding Site BS01

Receptor Information
>3k5x Chain A (length=391) Species: 1902 (Streptomyces coelicolor) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTSLEKARELLREFPVVDGHNDLPWALREQVRYDLDARDIAADQSAHLHT
DLARLRSGGVGAQYWSVYVRSDLPGAVTATLEQIDCVRRLIDRHPGELRA
ALTAADMEAARAEGRIASLMGAEGGHSIDNSLATLRALYALGVRYMTLTH
NDNNAWADSATDEPGVGGLSAFGREVVREMNREGMLVDLSHVAATTMRDA
LDTSTAPVIFSHSSSRAVCDHPRNIPDDVLERLSANGGMAMVTFVPKFVL
QAAVDWTAEADDNMRAHGFHHLDSSPEAMKVHAAFEERVPRPVATVSTVA
DHLDHMREVAGVDHLGIGGDYDGTPFTPDGLGDVSGYPNLIAELLDRGWS
QSDLAKLTWKNAVRVLDAAEDVSRGLRAARGPSNATIEQLD
Ligand information
Ligand IDP8D
InChIInChI=1S/C7H14NO6P/c1-4(8)15(13,14)3-5(7(11)12)2-6(9)10/h4-5H,2-3,8H2,1H3,(H,9,10)(H,11,12)(H,13,14)/t4-,5+/m1/s1
InChIKeyLWODXTSWCZWQHR-UHNVWZDZSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[C@H](N)[P](O)(=O)C[C@H](CC(O)=O)C(O)=O
CACTVS 3.352C[CH](N)[P](O)(=O)C[CH](CC(O)=O)C(O)=O
ACDLabs 11.02O=P(O)(C(N)C)CC(C(=O)O)CC(=O)O
OpenEye OEToolkits 1.7.0CC(N)P(=O)(CC(CC(=O)O)C(=O)O)O
OpenEye OEToolkits 1.7.0C[C@H](N)[P@@](=O)(C[C@H](CC(=O)O)C(=O)O)O
FormulaC7 H14 N O6 P
Namephosphinate pseudodipeptide L-Ala-D-Asp;
(2R)-2-{[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]methyl}butanedioic acid
ChEMBL
DrugBank
ZINCZINC000025109138
PDB chain3k5x Chain A Residue 401 [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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PDB3k5x Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
Resolution1.4 Å
Binding residue
(original residue number in PDB)		H20 D22 Y68 E123 H150 H191 H212 R223 F248 D320 G323 T324
Binding residue
(residue number reindexed from 1)		H20 D22 Y68 E123 H150 H191 H212 R223 F248 D320 G323 T324
Annotation score1
Binding affinityMOAD: Ki=390nM
PDBbind-CN: -logKd/Ki=6.41,Ki=390nM
Enzymatic activity
Catalytic site (original residue number in PDB) H20 D22 E123 H150 H191 H212 D320
Catalytic site (residue number reindexed from 1) H20 D22 E123 H150 H191 H212 D320
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0046872 metal ion binding
GO:0070573 metallodipeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3k5x, PDBe:3k5x, PDBj:3k5x
PDBsum3k5x
PubMed20000809
UniProtQ93J45

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