8W30

Crystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.275 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AFAClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Design and Discovery of a Potent and Selective Inhibitor of Integrin alpha v beta 1.

Sabat, M.Carney, D.W.Hernandez-Torres, G.Gibson, T.S.Balakrishna, D.Zou, H.Xu, R.Chen, C.H.de Jong, R.Dougan, D.R.Qin, L.Bigi-Botterill, S.V.Chambers, A.Miura, J.Johnson, L.K.Ermolieff, J.Johns, D.Selimkhanov, J.Kwok, L.DeMent, K.Proffitt, C.Vu, P.Lindsey, E.A.Ivetac, T.Jennings, A.Wang, H.Manam, P.Santos, C.Fullenwider, C.Manohar, R.Flick, A.C.

(2024) J Med Chem 67: 10306-10320

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00743
  • Primary Citation of Related Structures:  
    8W30

  • PubMed Abstract: 

    Selective inhibition of the RGD (Arg-Gly-Asp) integrin αvβ1 has been recently identified as an attractive therapeutic approach for the treatment of liver fibrosis given its function, target expression, and safety profile. Our identification of a non-RGD small molecule lead followed by focused, systematic changes to the core structure utilizing a crystal structure, in silico modeling, and a tractable synthetic approach resulted in the identification of a potent small molecule exhibiting a remarkable affinity for αvβ1 relative to several other integrin isoforms measured. Azabenzimidazolone 25 demonstrated antifibrotic efficacy in an in vivo rat liver fibrosis model and represents a tool compound capable of further exploring the biological consequences of selective αvβ1 inhibition.


  • Organizational Affiliation

    Gastroenterology Drug Discovery Unit, Takeda Development Center Americas, Inc., 9625 Towne Centre Dr., San Diego, California 92121 United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-V heavy chain605Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRAVTNR
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens)
Explore P06756 
Go to UniProtKB:  P06756
PHAROS:  P06756
GTEx:  ENSG00000138448 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06756
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P06756-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-1456Homo sapiensMutation(s): 0 
Gene Names: ITGB1FNRBMDF2MSK12
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens)
Explore P05556 
Go to UniProtKB:  P05556
PHAROS:  P05556
GTEx:  ENSG00000150093 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05556
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P05556-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AFA (Subject of Investigation/LOI)
Query on A1AFA

Download Ideal Coordinates CCD File 
P [auth B]N-(2,4-dichlorobenzoyl)-L-phenylalanine
C16 H13 Cl2 N O3
KDUPLHIWRBQFEC-AWEZNQCLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.275 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.184α = 90
b = 148.212β = 103.18
c = 53.415γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AFAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release