249,324
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

1ZMJ|pdb_00001zmj

Crystal Structure of the Catalytic Domain of Factor XI in complex with 4-(guanidinomethyl)-phenylboronic acid

PDB DOI: https://doi.org/10.2210/pdb1ZMJ/pdb

Classification: HYDROLASE
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.223 (Depositor)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)

Starting Model:experimental
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Ligand Structure Quality Assessment

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

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.07.043
Primary Citation of 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.

Organizational Affiliation

Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC, One Kendall Square, Building 700, Cambridge, MA 02139, USA. tlazarova@medchempartners.com

Macromolecule Content

Total Structure Weight: 27.32 kDa
Atom Count: 2,107
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): 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HDB Query on HDB Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(R)-1-(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL)BENZYL)GUANIDINE C₁₁ H₁₆ B N₃ O₃ IIZOWFNBOXPJES-SNVBAGLBSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		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] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223 (Depositor)
R-Value Work: 0.201 (Depositor), 0.201 (DCC)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.775	α = 90
b = 120.775	β = 90
c = 120.775	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(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: 2017-10-11
Changes: Data collection
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: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary