1ZSL | pdb_00001zsl

Factor XI complexed with a pyrimidinone inhibitor

PDB DOI: https://doi.org/10.2210/pdb1ZSL/pdb

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

Deposited: 2005-05-24 Released: 2006-05-09
Deposition Author(s): Nagafuji, P., Jin, L., Rynkiewicz, M., Quinn, J., Bibbins, F., Meyers, H., Babine, R., Strickler, J., Abdel-Meguid, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.254 (Depositor), 0.250 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Pyrimidinone Inhibitors of a Thrombolytic Protease

Nagafuji, P., Jin, L., Rynkiewicz, M., Quinn, J., Bibbins, F., Meyers, H., Babine, R., Strickler, J., Abdel-Meguid, S.

To be published.

Macromolecule Content

Total Structure Weight: 27.38 kDa
Atom Count: 2,028
Modeled 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): 2 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
624 Query on 624 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-(2-(3,4-DICHLOROPHENYL)-5-(ISOPROPYLAMINO)-6-OXOPYRIMIDIN-1(6H)-YL)-N-((S)-1-OXO-1-(THIAZOL-2-YL)-5-GUANIDINOPENTAN-2-YL)ACETAMIDE C₂₄ H₂₈ Cl₂ N₈ O₃ S LJLKTQRJOBRXIB-KRWDZBQOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.254 (Depositor), 0.250 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.385	α = 90
b = 122.385	β = 90
c = 122.385	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Abdel-Meguid, S.

Revision History (Full details and data files)

Version 1.0: 2006-05-09
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-23
Changes: Data collection, Refinement description
Version 1.6: 2024-11-06
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.