1ZPC

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with 2-[2-(3-Chloro-phenyl)-2-hydroxy-acetylamino]-N-[4-guanidino-1-(thiazole-2-carbonyl)-butyl]-3-methyl-butyramide

PDB DOI: https://doi.org/10.2210/pdb1ZPC/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2005-05-16 Released: 2006-04-18
Deposition Author(s): Deng, H., Bannister, T.D., Jin, L., Nagafuji, P., Celatka, C.A., Lin, J., Lazarova, T.I., Rynkiewicz, M.J., Quinn, J., Bibbins, F., Pandey, P., Gorga, J., Babine, R.E., Meyers, H.V., Abdel-Meguid, S.S., Strickler, J.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.229
R-Value Work: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Synthesis, SAR exploration, and X-ray crystal structures of factor XIa inhibitors containing an alpha-ketothiazole arginine

Deng, H., Bannister, T.D., Jin, L., Babine, R.E., Quinn, J., Nagafuji, P., Celatka, C.A., Lin, J., Lazarova, T.I., Rynkiewicz, M.J., Bibbins, F., Pandey, P., Gorga, J., Meyers, H.V., Abdel-Meguid, S.S., Strickler, J.E.

(2006) Bioorg Med Chem Lett 16: 3049-3054

PubMed: 16524727 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.02.052
Primary Citation of Related Structures:
1ZPB, 1ZPC, 2FDA

PubMed Abstract:
Using an alpha-ketothiazole arginine moiety as a key recognition element, a series of small peptidomimetic molecules was designed and synthesized, and their co-crystal structures with factor XIa were studied in an effort to develop smaller, less peptidic inhibitors as antithrombotic agents.

Organizational Affiliation

Department of Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC (DAIAMED), One Kendall Square, Bldg 700, Cambridge, MA 02139, USA. hongfeng.deng@praecis.com

Macromolecule Content

Total Structure Weight: 27.55 kDa
Atom Count: 1,999
Modelled Residue Count: 237
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	238	Homo sapiens	Mutation(s): 4 Gene Names: F11 EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens) Explore P03951 Go to UniProtKB: P03951
PHAROS: P03951 GTEx: ENSG00000088926
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03951
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
716 Query on 716 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	2-[2-(3-CHLORO-PHENYL)-2-HYDROXY-ACETYLAMINO]-N-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYL]-3-METHYL-BUTYRAMIDE C₂₂ H₂₇ Cl N₆ O₄ S NZMZDRVEUJTADA-HOTGVXAUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]