Structure of PDB 3bpc Chain A Binding Site BS02

Receptor Information

>3bpc Chain A (length=216) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSP
KLLIYWASTRESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYNL
RTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDIN
VKWKIDGSEGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATH
KTSTSPIVKSFNRNEC

Ligand information

Ligand ID

KDB

InChI

InChI=1S/C8H12O6/c9-4-5(10)6-2-1-3-8(13,14-6)7(11)12/h1,3,5-6,9-10,13H,2,4H2,(H,11,12)/t5-,6+,8-/m1/s1

InChIKey

ITFIFEKDEVIBCW-GKROBHDKSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	C1C=C[C@@](O[C@@H]1[C@@H](CO)O)(C(=O)O)O
CACTVS 3.385	OC[CH](O)[CH]1CC=C[C](O)(O1)C(O)=O
ACDLabs 12.01	OC1(C(=O)O)C=CCC(C(CO)O)O1
OpenEye OEToolkits 2.0.7	C1C=CC(OC1C(CO)O)(C(=O)O)O
CACTVS 3.385	OC[C@@H](O)[C@@H]1CC=C[C@@](O)(O1)C(O)=O

Formula

C8 H12 O6

Name

3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid;
3,4-dehydro-3,4,5-trideoxy-alpha-D-manno-oct-2-ulosonic acid;
3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulosonic acid;
3,4,5-trideoxy-D-erythro-oct-3-en-2-ulosonic acid;
3,4,5-trideoxy-erythro-oct-3-en-2-ulosonic acid

PDB chain

3bpc Chain C Residue 2 [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	3bpc Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.
Resolution	1.85 Å
Binding residue (original residue number in PDB)	N30A R30C
Binding residue (residue number reindexed from 1)	N31 R33
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=4.80,Kd=16uM

External links

PDB	RCSB:3bpc, PDBe:3bpc, PDBj:3bpc
PDBsum	3bpc
PubMed	18272175

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