1ZML | pdb_00001zml

Crystal Structure of the Catalytic Domain of Factor XI in complex with (R)-1-(4-(4-(hydroxymethyl)-1,3,2-dioxaborolan-2-yl)phenethyl)guanidine

• PDB DOI: https://doi.org/10.2210/pdb1ZML/pdb

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


• Deposited: 2005-05-10 Released: 2006-05-09 
• Deposition Author(s): Lazarova, T.I., Jin, L., Rynkiewicz, M.J., Gorga, J.C., Bibbins, F., Meyers, H.V., Babine, R.E., Strickler, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.202 (DCC) 

Starting Model: experimental

Literature

Synthesis and in vitro biological evaluation of aryl boronic acids as potential inhibitors of factor XIa.

Lazarova, T.I., Jin, L., Rynkiewicz, M., Gorga, J.C., Bibbins, F., Meyers, H.V., Babine, R., Strickler, J.

(2006) Bioorg Med Chem Lett 16: 5022-5027

• PubMed: 16876411 
• DOI: https://doi.org/10.1016/j.bmcl.2006.07.043
• Primary Citation Related Structures: 
  1ZLR, 1ZMJ, 1ZML, 1ZMN


• PubMed Abstract: 
  

  A series of functionalized aryl boronic acids were synthesized and evaluated as potential inhibitors of factor XIa. Crystal structures of the protein-inhibitor complexes led to the design and synthesis of second generation compounds showing single digit micromolar inhibition against FXIa and selectivity against thrombin, trypsin, and FXa.

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Organizational Affiliation: 
• Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC, One Kendall Square, Building 700, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.65 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 237 
• 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
412	I [auth A]	(R)-1-(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL)PHENETHYL)GUANIDINE C12 H18 B N3 O3 ZYCNKSJMJFKCBX-LLVKDONJSA-N
SO4	B [auth A], C [auth A], D [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BCT	E [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.229 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.202 (DCC) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.291	α = 90
b = 121.291	β = 90
c = 121.291	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: 2006-05-09 
Deposition Author(s): Lazarova, T.I., Jin, L., Rynkiewicz, M.J., Gorga, J.C., Bibbins, F., Meyers, H.V., Babine, R.E., Strickler, J.E.

Revision History  

• 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: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary