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Structure of PDB 2cmc Chain A Binding Site BS01

Receptor Information

>2cmc Chain A (length=285) Species: 9606 (Homo sapiens)

HHHHHHEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNR
YRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHF
WEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLI
SEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFL
FKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVD
IKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKF

Ligand information

• Ligand ID: DFM
• InChI: InChI=1S/C21H24F2N3O6P/c1-13(27)25-18(12-14-5-3-2-4-6-14)20(29)26-17(19(24)28)11-15-7-9-16(10-8-15)21(22,23)33(30,31)32/h2-10,17-18H,11-12H2,1H3,(H2,24,28)(H,25,27)(H,26,29)(H2,30,31,32)/t17-,18-/m0/s1
• InChIKey: KPMMESISHWWXNM-ROUUACIJSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(cc2)C(F)(F)[P](O)(O)=O)C(N)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC(Cc1ccccc1)C(=O)NC(Cc2ccc(cc2)C(F)(F)P(=O)(O)O)C(=O)N
  CACTVS 3.341: CC(=O)N[CH](Cc1ccccc1)C(=O)N[CH](Cc2ccc(cc2)C(F)(F)[P](O)(O)=O)C(N)=O
  ACDLabs 10.04: FC(F)(c1ccc(cc1)CC(C(=O)N)NC(=O)C(NC(=O)C)Cc2ccccc2)P(=O)(O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(cc2)C(F)(F)P(=O)(O)O)C(=O)N
• Formula: C21 H24 F2 N3 O6 P
• Name: N-ACETYL-L-PHENYLALANYL-4-[DIFLUORO(PHOSPHONO)METHYL]-L-PHENYLALANINAMIDE;
  DIFLUOROMETHYLPHOSPHONIC ACID ANALOG
• ChEMBL: CHEMBL196526
• DrugBank: DB07651
• ZINC: ZINC000013674405
• PDB chain: 2cmc Chain A Residue 1281

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2cmc Structural Basis for Inhibition of Protein-Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): Y46 R47 D48 V49 F182 C215 S216 A217 I219 G220 R221 Q262 K279 F280
• Binding residue (residue number reindexed from 1): Y51 R52 D53 V54 F187 C220 S221 A222 I224 G225 R226 Q267 K284 F285
• Annotation score: 1
• Binding affinity: MOAD: ic50=1750nM
  PDBbind-CN: -logKd/Ki=5.76,IC50=1.75uM
  BindingDB: IC50=1750nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D181 C215 R221 S222 Q262
• Catalytic site (residue number reindexed from 1): D186 C220 R226 S227 Q267
• Enzyme Commision number: 3.1.3.48: protein-tyrosine-phosphatase.

Gene Ontology

Molecular Function

• GO:0004725 protein tyrosine phosphatase activity

Biological Process

• GO:0006470 protein dephosphorylation
• GO:0016311 dephosphorylation

External links

• PDB: RCSB:2cmc, PDBe:2cmc, PDBj:2cmc
• PDBsum: 2cmc
• PubMed: 16916797
• UniProt: P18031|PTN1_HUMAN Tyrosine-protein phosphatase non-receptor type 1 (Gene Name=PTPN1)

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