Structure of PDB 3m6f Chain A Binding Site BS01

Receptor Information

>3m6f Chain A (length=180) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSY
KTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGAR
PDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKF
ASKPASEFVKILDTFEKLKDLFTELQKKIY

Ligand information

Ligand ID

BJZ

InChI

InChI=1S/C26H19Cl2N5O4/c1-31-25(37)33(20-9-18(27)8-19(28)10-20)24(36)26(31)14-32(22-7-6-17(12-30-22)23(34)35)13-21(26)16-4-2-15(11-29)3-5-16/h2-10,12,21H,13-14H2,1H3,(H,34,35)/t21-,26+/m0/s1

InChIKey

LILGMDXLRPEBNH-HFZDXXHNSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	CN1C(=O)N(C(=O)[C@]12CN(C[C@H]2c3ccc(cc3)C#N)c4ccc(cn4)C(=O)O)c5cc(cc(c5)Cl)Cl
ACDLabs 12.01	O=C(O)c1ccc(nc1)N5CC(c2ccc(C#N)cc2)C3(C(=O)N(C(=O)N3C)c4cc(Cl)cc(Cl)c4)C5
OpenEye OEToolkits 1.7.0	CN1C(=O)N(C(=O)C12CN(CC2c3ccc(cc3)C#N)c4ccc(cn4)C(=O)O)c5cc(cc(c5)Cl)Cl
CACTVS 3.370	CN1C(=O)N(C(=O)[C@]12CN(C[C@H]2c3ccc(cc3)C#N)c4ccc(cn4)C(O)=O)c5cc(Cl)cc(Cl)c5
CACTVS 3.370	CN1C(=O)N(C(=O)[C]12CN(C[CH]2c3ccc(cc3)C#N)c4ccc(cn4)C(O)=O)c5cc(Cl)cc(Cl)c5

Formula

C26 H19 Cl2 N5 O4

Name

6-[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non-7-yl]pyridine-3-carboxylic acid

PDB chain

3m6f Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3m6f Small molecule antagonist of leukocyte function associated antigen-1 (LFA-1): structure-activity relationships leading to the identification of 6-((5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]nonan-7-yl)nicotinic acid (BMS-688521).
Resolution	1.85 Å
Binding residue (original residue number in PDB)	V157 Y166 T231 I235 Y257 I259 K287 L302 I306
Binding residue (residue number reindexed from 1)	V30 Y39 T104 I108 Y130 I132 K160 L175 I179
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=8.60,IC50=2.5nM BindingDB: IC50=60nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:3m6f, PDBe:3m6f, PDBj:3m6f
PDBsum	3m6f
PubMed	20405922
UniProt	P20701\|ITAL_HUMAN Integrin alpha-L (Gene Name=ITGAL)

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