1ZSJ

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in complex with N-(7-Carbamimidoyl-naphthalen-1-yl)-3-hydroxy-2-methyl-benzamide

• PDB DOI: https://doi.org/10.2210/pdb1ZSJ/pdb

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


• Deposited: 2005-05-24 Released: 2006-05-23 
• Deposition Author(s): Guo, Z., Bannister, T., Noll, R., Jin, L., Rynkiewicz, M., Bibbins, F., Magee, S., Gorga, J., Babine, R.E., Strickler, J.E., Meyers, H.V., Abdel-Meguid, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.188 

Starting Model: experimental

Literature

Synthesis and Optimization of Potent and Selective Inhibitors for Human Factor XIa: Substituted Naphthamidine Series

Guo, Z., Bannister, T., Noll, R., Jin, L., Rynkiewicz, M., Bibbins, F., Magee, S., Gorga, J., Babine, R.E., Strickler, J.E., Meyers, H.V., Abdel-Meguid, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.23 kDa 
• Atom Count: 2,188 
• Modelled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
709	D [auth A]	N-(7-CARBAMIMIDOYL-NAPHTHALEN-1-YL)-3-HYDROXY-2-METHYL-BENZAMIDE C19 H17 N3 O2 NNGZRCYXFBHMRM-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BCT	C [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.188 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.74	α = 90
b = 120.74	β = 90
c = 120.74	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-23 
Deposition Author(s): Guo, Z., Bannister, T., Noll, R., Jin, L., Rynkiewicz, M., Bibbins, F., Magee, S., Gorga, J., Babine, R.E., Strickler, J.E., Meyers, H.V., Abdel-Meguid, S.S.

Revision History  

• Version 1.0: 2006-05-23
  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: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary