Structure of PDB 1nny Chain A Binding Site BS01

Receptor Information
>1nny Chain A (length=282) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSP
FDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWE
QKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKS
YYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES
GSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLL
EMRKFRMGLIQTADQLRFSYLAVIEGAKFIMG
Ligand information
Ligand ID515
InChIInChI=1S/C40H37N3O10/c1-24(44)42-32(36(45)41-19-9-2-10-20-53-35-23-26-12-4-3-11-25(26)21-31(35)39(49)50)22-27-17-18-34(29-14-6-5-13-28(27)29)43(37(46)40(51)52)33-16-8-7-15-30(33)38(47)48/h3-8,11-18,21,23,32H,2,9-10,19-20,22H2,1H3,(H,41,45)(H,42,44)(H,47,48)(H,49,50)(H,51,52)/t32-/m0/s1
InChIKeyURRKGBLRIVECAH-YTTGMZPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH](Cc1ccc(N(C(=O)C(O)=O)c2ccccc2C(O)=O)c3ccccc13)C(=O)NCCCCCOc4cc5ccccc5cc4C(O)=O
CACTVS 3.341CC(=O)N[C@@H](Cc1ccc(N(C(=O)C(O)=O)c2ccccc2C(O)=O)c3ccccc13)C(=O)NCCCCCOc4cc5ccccc5cc4C(O)=O
ACDLabs 10.04O=C(O)c1ccccc1N(C(=O)C(=O)O)c3c2c(cccc2)c(cc3)CC(NC(=O)C)C(=O)NCCCCCOc5c(cc4c(cccc4)c5)C(=O)O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H](Cc1ccc(c2c1cccc2)N(c3ccccc3C(=O)O)C(=O)C(=O)O)C(=O)NCCCCCOc4cc5ccccc5cc4C(=O)O
OpenEye OEToolkits 1.5.0CC(=O)NC(Cc1ccc(c2c1cccc2)N(c3ccccc3C(=O)O)C(=O)C(=O)O)C(=O)NCCCCCOc4cc5ccccc5cc4C(=O)O
FormulaC40 H37 N3 O10
Name3-({5-[(N-ACETYL-3-{4-[(CARBOXYCARBONYL)(2-CARBOXYPHENYL)AMINO]-1-NAPHTHYL}-L-ALANYL)AMINO]PENTYL}OXY)-2-NAPHTHOIC ACID;
COMPOUND 23
ChEMBLCHEMBL1230341
DrugBank
ZINCZINC000024633064
PDB chain1nny Chain A Residue 322 [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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PDB1nny Discovery of a Potent, Selective Protein Tyrosine Phosphatase 1B Inhibitor Using a Linked-Fragment Strategy
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R24 Y46 D48 K120 C215 S216 A217 I219 G220 R221 R254 Q262 T263 G283
Binding residue
(residue number reindexed from 1)		R23 Y45 D47 K119 C214 S215 A216 I218 G219 R220 R253 Q261 T262 G282
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.66,Ki=22nM
BindingDB: Ki=20nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1nny, PDBe:1nny, PDBj:1nny
PDBsum1nny
PubMed12670229
UniProtP18031|PTN1_HUMAN Tyrosine-protein phosphatase non-receptor type 1 (Gene Name=PTPN1)

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