8W30 | pdb_00008w30

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

Validation slider image for 8W30

Ligand Structure Quality Assessment 


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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 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.

Macromolecule Content 

  • Total Structure Weight: 120.6 kDa 
  • Atom Count: 7,551 
  • Modeled Residue Count: 954 
  • Deposited Residue Count: 1,061 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
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Reference Sequence
Find similar proteins by:|  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 GlycosylationD 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 GlycosylationD 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]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [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 


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