Structure of PDB 4yhi Chain H Binding Site BS01

Receptor Information
>4yhi Chain H (length=222) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYYMHWVRQAPGQGLEWMGE
TNPRNGGTTYNEKFKGKATMTRDTSTSTAYMELSSLRSEDTAVYYCTIGT
SGYDYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKD
YFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTY
ICNVNHKPSNTKVDKKVEPKSC
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 chain4yhi 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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PDB4yhi Structure-guided residence time optimization of a dabigatran reversal agent.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D31 Y33 H35 E50 N52 R54 Y103 D104 Y105 F106
Binding residue
(residue number reindexed from 1)		D31 Y33 H35 E50 N52 R54 Y103 D104 Y105 F106
Annotation score1
Binding affinityMOAD: ic50=4.6nM
External links