Structure of PDB 1nl9 Chain A Binding Site BS01

Receptor Information

>1nl9 Chain A (length=282) Species: 9606 (Homo sapiens)

EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSP
FDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWE
QKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKS
YYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES
GSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLL
EMRKFRMGLIQTADQLRFSYLAVIEGAKFIMG

Ligand information

• Ligand ID: 989
• InChI: InChI=1S/C29H31N3O7/c1-3-4-9-16-30-26(34)23(31-18(2)33)17-19-14-15-25(21-11-6-5-10-20(19)21)32(27(35)29(38)39)24-13-8-7-12-22(24)28(36)37/h5-8,10-15,23H,3-4,9,16-17H2,1-2H3,(H,30,34)(H,31,33)(H,36,37)(H,38,39)/t23-/m0/s1
• InChIKey: UESXELNYBIOROE-QHCPKHFHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCNC(=O)C(Cc1ccc(c2c1cccc2)N(c3ccccc3C(=O)O)C(=O)C(=O)O)NC(=O)C
  CACTVS 3.341: CCCCCNC(=O)[CH](Cc1ccc(N(C(=O)C(O)=O)c2ccccc2C(O)=O)c3ccccc13)NC(C)=O
  CACTVS 3.341: CCCCCNC(=O)[C@H](Cc1ccc(N(C(=O)C(O)=O)c2ccccc2C(O)=O)c3ccccc13)NC(C)=O
  OpenEye OEToolkits 1.5.0: CCCCCNC(=O)[C@H](Cc1ccc(c2c1cccc2)N(c3ccccc3C(=O)O)C(=O)C(=O)O)NC(=O)C
  ACDLabs 10.04: O=C(N(c2c1ccccc1c(cc2)CC(C(=O)NCCCCC)NC(=O)C)c3ccccc3C(=O)O)C(=O)O
• Formula: C29 H31 N3 O7
• Name: 2-{[4-(2-ACETYLAMINO-2-PENTYLCARBAMOYL-ETHYL)-NAPHTHALEN-1-YL]-OXALYL-AMINO}-BENZOIC ACID;
  COMPOUND 12;
  N-ACETYL-4-[(CARBOXYCARBONYL)(2-CARBOXYPHENYL)AMINO]-N-PENTYL-1-NAPTHYLALANIAMIDE
• ChEMBL: CHEMBL1230658
• DrugBank: DB01820
• ZINC: ZINC000014880083
• PDB chain: 1nl9 Chain A Residue 322

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1nl9 Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): Y46 D48 C215 S216 A217 I219 G220 R221 Q262 T263 G283
• Binding residue (residue number reindexed from 1): Y45 D47 C214 S215 A216 I218 G219 R220 Q261 T262 G282
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.96,Ki=1.1uM
  BindingDB: Ki=631nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D181 C215 R221 S222 Q262
• Catalytic site (residue number reindexed from 1): D180 C214 R220 S221 Q261
• 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:1nl9, PDBe:1nl9, PDBj:1nl9
• PDBsum: 1nl9
• PubMed: 12670229
• UniProt: P18031|PTN1_HUMAN Tyrosine-protein phosphatase non-receptor type 1 (Gene Name=PTPN1)