6MK0

Integrin AlphaVBeta3 ectodomain bound to antagonist TDI-4161


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report



Literature

Novel Pure alphaVbeta3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations

Li, J.Fukase, Y.Shang, Y.Zou, W.Munoz-Felix, J.Buitrago, L.van Agthoven, J.Zhang, Y.Hara, R.Tanaka, Y.Okamoto, R.Yasui, T.Nakahata, T.Imaeda, T.Aso, K.Zhou, Y.Locuson, C.Nesic, D.Duggan, M.Takagi, J.Vaughan, R.D.Walz, T.Hodivala-Dilke, K.Teitelbaum, S.L.Arnaout, M.A.Filizola, M.Foley, M.A.Coller, B.S.

(2019) Acs Pharmacol Transl Sci 2: 387-401


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-VA954Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRAVTNR
Find proteins for P06756 (Homo sapiens)
Explore P06756 
Go to UniProtKB:  P06756
NIH Common Fund Data Resources
PHAROS  P06756
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-3B687Homo sapiensMutation(s): 0 
Gene Names: ITGB3GP3A
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS  P05106
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, F, G
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-beta-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
6 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain 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
H
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JUY
Query on JUY

Download CCD File 
B
(2S)-2-[(1,3-benzothiazole-2-carbonyl)amino]-4-{[5-(1,8-naphthyridin-2-yl)pentanoyl]amino}butanoic acid
C25 H25 N5 O4 S
WHGYZWMTBKTNLT-IBGZPJMESA-N
 Ligand Interaction
NAG
Query on NAG

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A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.406α = 90
b = 129.406β = 90
c = 305.535γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesK01DK101628-04

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 2.0: 2019-10-23
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2019-11-20
    Changes: Derived calculations
  • Version 2.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.3: 2020-02-12
    Changes: Data collection, Database references, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary