Structure of PDB 1rd4 Chain D Binding Site BS01

Receptor Information

>1rd4 Chain D (length=184) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSY
KTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGAR
PDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKF
ASKPASEFVKILDTFEKLKDLFTELQKKIYVIEG

Ligand information

Ligand ID

L08

InChI

InChI=1S/C25H26N4O4S/c1-3-33-22-6-4-5-7-24(22)34-23-9-8-19(16-21(23)29(31)32)20-10-11-26-25(17-20)28-14-12-27(13-15-28)18(2)30/h4-11,16-17H,3,12-15H2,1-2H3

InChIKey

GKGJFUXSTSUKPB-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CCOc1ccccc1Sc2ccc(cc2[N+](=O)[O-])c3ccnc(c3)N4CCN(CC4)C(=O)C
ACDLabs 10.04	[O-][N+](=O)c2c(Sc1ccccc1OCC)ccc(c2)c3cc(ncc3)N4CCN(C(=O)C)CC4
CACTVS 3.341	CCOc1ccccc1Sc2ccc(cc2[N+]([O-])=O)c3ccnc(c3)N4CCN(CC4)C(C)=O

Formula

C25 H26 N4 O4 S

Name

1-ACETYL-4-(4-{4-[(2-ETHOXYPHENYL)THIO]-3-NITROPHENYL}PYRIDIN-2-YL)PIPERAZINE

PDB chain

1rd4 Chain D Residue 3328 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	1rd4 Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry
Resolution	2.4 Å
Binding residue (original residue number in PDB)	F153 Y166 I235 Y257 I259 E284 F285 V286 K287 L298 E301 L302 K305
Binding residue (residue number reindexed from 1)	F26 Y39 I108 Y130 I132 E157 F158 V159 K160 L171 E174 L175 K178
Annotation score	1
Binding affinity	MOAD: Kd=18.3nM BindingDB: Kd=18nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:1rd4, PDBe:1rd4, PDBj:1rd4
PDBsum	1rd4
PubMed	14992576
UniProt	P20701\|ITAL_HUMAN Integrin alpha-L (Gene Name=ITGAL)

[Back to BioLiP]