Structure of PDB 1nd5 Chain C Binding Site BS01

Receptor Information
>1nd5 Chain C (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KELKFVTLVFRHGDRSPIDTFPTDPIKESSWPQGFGQLTQLGMEQHYELG
EYIRKRYRKFLNESYKHEQVYIRSTDVDRTLMSAMTNLAALFPPEGVSIW
NPILLWQPIPVHTVPLSEDQLLYLPFRNCPRFQELESETLKSEEFQKRLH
PYKDFIATLGKLSGLHGQDLFGIWSKVYDPLYCESVHNFTLPSWATEDTM
TKLRELSELSLLSLYGIHKQKEKSRLQGGVLVNEILNHMKRATQIPSYKK
LIMYSAHDTTVSGLQMALDVYNGLLPPYASCHLTELYFEKGEYFVEMYYR
NETQHEPYPLMLPGCSPSCPLERFAELVGPVIPQDWSTECMT
Ligand information
Ligand ID2BF
InChIInChI=1S/C14H16NO3P/c16-19(17,18)14(13-9-5-2-6-10-13)15-11-12-7-3-1-4-8-12/h1-10,14-15H,11H2,(H2,16,17,18)/t14-/m1/s1
InChIKeySLMGIUOAZCYKPE-CQSZACIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[P](O)(=O)[C@@H](NCc1ccccc1)c2ccccc2
CACTVS 3.341O[P](O)(=O)[CH](NCc1ccccc1)c2ccccc2
OpenEye OEToolkits 1.5.0c1ccc(cc1)CNC(c2ccccc2)P(=O)(O)O
OpenEye OEToolkits 1.5.0c1ccc(cc1)CN[C@@H](c2ccccc2)P(=O)(O)O
ACDLabs 10.04O=P(O)(O)C(NCc1ccccc1)c2ccccc2
FormulaC14 H16 N O3 P
NameALPHA-BENZYL-AMINOBENZYL-PHOSPHONIC ACID
ChEMBLCHEMBL1186230
DrugBankDB03577
ZINC
PDB chain1nd5 Chain C Residue 6002 [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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PDB1nd5 Crystal structures of human prostatic acid phosphatase in complex with a phosphate ion and alpha-benzylaminobenzylphosphonic acid update the mechanistic picture and offer new insights into inhibitor design
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R2010 H2011 R2014 I2017 R2078 Y2122 S2174 H2256 D2257 T2258
Binding residue
(residue number reindexed from 1)		R11 H12 R15 I18 R79 Y123 S175 H257 D258 T259
Annotation score1
Binding affinityBindingDB: IC50=4nM
Enzymatic activity
Enzyme Commision number 3.1.3.2: acid phosphatase.
3.1.3.48: protein-tyrosine-phosphatase.
3.1.3.5: 5'-nucleotidase.
Gene Ontology
Molecular Function
GO:0003993 acid phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0008253 5'-nucleotidase activity
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0033265 choline binding
GO:0042131 thiamine phosphate phosphatase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0052642 lysophosphatidic acid phosphatase activity
GO:0060090 molecular adaptor activity
GO:0106411 XMP 5'-nucleosidase activity
Biological Process
GO:0006144 purine nucleobase metabolic process
GO:0006629 lipid metabolic process
GO:0006772 thiamine metabolic process
GO:0007040 lysosome organization
GO:0009117 nucleotide metabolic process
GO:0016311 dephosphorylation
GO:0046085 adenosine metabolic process
GO:0051930 regulation of sensory perception of pain
GO:0060168 positive regulation of adenosine receptor signaling pathway
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005771 multivesicular body
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012506 vesicle membrane
GO:0016020 membrane
GO:0030141 secretory granule
GO:0030175 filopodium
GO:0031985 Golgi cisterna
GO:0035577 azurophil granule membrane
GO:0045177 apical part of cell
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1nd5, PDBe:1nd5, PDBj:1nd5
PDBsum1nd5
PubMed12525165
UniProtP15309|PPAP_HUMAN Prostatic acid phosphatase (Gene Name=ACP3)

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