Structure of PDB 4yhk Chain H Binding Site BS01

Receptor Information
>4yhk 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 chain4yhk 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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PDB4yhk Structure-guided residence time optimization of a dabigatran reversal agent.
Resolution2.21 Å
Binding residue
(original residue number in PDB)		Y33 H35 E50 Y103 D104 Y105 F106
Binding residue
(residue number reindexed from 1)		Y33 H35 E50 Y103 D104 Y105 F106
Annotation score1
Binding affinityMOAD: ic50=4.6nM
External links