Structure of PDB 4yho Chain L Binding Site BS01

Receptor Information
>4yho Chain L (length=219) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIVMTQTPLSLSVTPGQPASISCRSSQSIVHSDGNIYLEWYLQKPGQSPK
LLIYKVSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQASHVP
YTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK
VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACE
VTHQGLSSPVTKSFNRGEC
Ligand information
Ligand ID4CC
InChIInChI=1S/C25H25N7O3/c1-31-20-10-7-17(25(35)32(13-11-23(33)34)21-4-2-3-12-28-21)14-19(20)30-22(31)15-29-18-8-5-16(6-9-18)24(26)27/h2-10,12,14,29H,11,13,15H2,1H3,(H3,26,27)(H,33,34)
InChIKeyYBSJFWOBGCMAKL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2[H]/N=C(\c1ccc(cc1)NCc2nc3cc(ccc3n2C)C(=O)N(CCC(=O)O)c4ccccn4)/N
ACDLabs 12.01n2(C)c(CNc1ccc(cc1)/C(N)=N)nc3cc(ccc23)C(N(c4ncccc4)CCC(=O)O)=O
OpenEye OEToolkits 1.9.2Cn1c2ccc(cc2nc1CNc3ccc(cc3)C(=N)N)C(=O)N(CCC(=O)O)c4ccccn4
CACTVS 3.385Cn1c(CNc2ccc(cc2)C(N)=N)nc3cc(ccc13)C(=O)N(CCC(O)=O)c4ccccn4
FormulaC25 H25 N7 O3
NameN-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine
ChEMBLCHEMBL48361
DrugBankDB14726
ZINCZINC000001910616
PDB chain4yho Chain H Residue 301 [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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PDB4yho Structure-guided residence time optimization of a dabigatran reversal agent.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		E39 A96
Binding residue
(residue number reindexed from 1)		E39 A96
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.74,Kd=18pM
External links