Structure of PDB 4yhm Chain H Binding Site BS01

Receptor Information

>4yhm 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 ID

4CC

InChI

InChI=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)

InChIKey

YBSJFWOBGCMAKL-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.9.2	[H]/N=C(\c1ccc(cc1)NCc2nc3cc(ccc3n2C)C(=O)N(CCC(=O)O)c4ccccn4)/N
ACDLabs 12.01	n2(C)c(CNc1ccc(cc1)/C(N)=N)nc3cc(ccc23)C(N(c4ncccc4)CCC(=O)O)=O
OpenEye OEToolkits 1.9.2	Cn1c2ccc(cc2nc1CNc3ccc(cc3)C(=N)N)C(=O)N(CCC(=O)O)c4ccccn4
CACTVS 3.385	Cn1c(CNc2ccc(cc2)C(N)=N)nc3cc(ccc13)C(=O)N(CCC(O)=O)c4ccccn4

Formula

C25 H25 N7 O3

Name

N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine

PDB chain

4yhm Chain H Residue 301 [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	4yhm Structure-guided residence time optimization of a dabigatran reversal agent.
Resolution	2.16 Å
Binding residue (original residue number in PDB)	D31 Y33 H35 E50 N52 R54 Y103 Y105 F106
Binding residue (residue number reindexed from 1)	D31 Y33 H35 E50 N52 R54 Y103 Y105 F106
Annotation score	1
Binding affinity	MOAD: Kd=173pM PDBbind-CN: -logKd/Ki=9.76,Kd=173pM

External links

PDB	RCSB:4yhm, PDBe:4yhm, PDBj:4yhm
PDBsum	4yhm
PubMed	26047352

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