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Structure paper

TitleA general chemical principle for creating closure-stabilizing integrin inhibitors.
Journal, issue, pagesCell, Vol. 185, Page 3533-3550.e27, Year 2022
Publish dateDec 31, 2020 (structure data deposition date)
AuthorsLin, F.Y. / Li, J. / Xie, Y. / Zhu, J. / Huong Nguyen, T.T. / Zhang, Y. / Springer, T.A.
External linksCell / PubMed:36113427
MethodsX-ray diffraction
Resolution1.99998841007 - 2.99768170407 Å
Structure data

PDB-7l8p:
Integrin alphaIIbbeta3 in complex with sibrafiban
Method: X-RAY DIFFRACTION / Resolution: 2.3499537016 Å

PDB-7tct:
Integrin alpha IIB beta3 complex with UR2922
Method: X-RAY DIFFRACTION / Resolution: 2.501 Å

PDB-7td8:
Integrin alpha IIB beta3 complex with Tirofiban
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-7tho:
Integrin alpha IIB beta3 complex with Eptifibatide
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-7tmz:
Integrin alpha IIB beta3 complex with BMS compound 4
Method: X-RAY DIFFRACTION / Resolution: 2.20001999293 Å

PDB-7tpd:
Integrin alpha IIB beta3 complex with EF5154
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-7u60:
Integrin alpha IIB beta3 complex with cRGDfV
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-7u9f:
Integrin alpha IIB beta3 complex with BMS compound 4 in Mn2+
Method: X-RAY DIFFRACTION / Resolution: 2.70000525883 Å

PDB-7u9v:
Integrin alpha IIB beta3 complex with BMS4-1
Method: X-RAY DIFFRACTION / Resolution: 2.25492157575 Å

PDB-7ubr:
Integrin alpha IIB beta3 complex with GR144053
Method: X-RAY DIFFRACTION / Resolution: 2.04992751372 Å

PDB-7ucy:
Integrin alpha IIB beta3 complex with gantofiban
Method: X-RAY DIFFRACTION / Resolution: 2.34996314573 Å

PDB-7udg:
Integrin alpha IIB beta3 complex with lotrafiban
Method: X-RAY DIFFRACTION / Resolution: 2.80006901797 Å

PDB-7udh:
Integrin alpha IIB beta3 complex with BMS4-3
Method: X-RAY DIFFRACTION / Resolution: 1.99998841007 Å

PDB-7ue0:
Integrin alpha IIB beta3 complex with fradafiban
Method: X-RAY DIFFRACTION / Resolution: 2.74196193977 Å

PDB-7ufh:
Integrin alpha IIB beta3 complex with fradafiban (Mn/Ca)
Method: X-RAY DIFFRACTION / Resolution: 2.99768170407 Å

PDB-7uh8:
Integrin alpha IIB beta3 complex with roxifiban (Mn/Ca)
Method: X-RAY DIFFRACTION / Resolution: 2.75002413567 Å

PDB-7uje:
Integrin alpha IIB beta3 complex with UR2922 in Mn2+
Method: X-RAY DIFFRACTION / Resolution: 2.4999681528 Å

PDB-7ujk:
Integrin alpha IIB beta3 complex with lamifiban
Method: X-RAY DIFFRACTION / Resolution: 2.43265583434 Å

PDB-7uk9:
Integrin alpha IIB beta3 complex with lamifiban (Mn)
Method: X-RAY DIFFRACTION / Resolution: 2.60001966299 Å

PDB-7uko:
Integrin alpha IIB beta3 complex with sibrafiban (Mn)
Method: X-RAY DIFFRACTION / Resolution: 2.604 Å

PDB-7ukp:
Integrin alpha IIB beta3 complex with a gantofiban analog
Method: X-RAY DIFFRACTION / Resolution: 2.80112979054 Å

PDB-7ukt:
Integrin alpha IIB beta3 complex with BMS4.2
Method: X-RAY DIFFRACTION / Resolution: 2.36994437552 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-GOL:
GLYCEROL

ChemComp-CA:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-XQS:
sibrafiban (active form) / inhibitor*YM

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-I1F:
{5-[N-(4-carbamimidoylbenzoyl)-4-nitro-L-phenylalanyl]-4,5,6,7-tetrahydro-2H-pyrazolo[4,3-c]pyridin-2-yl}acetic acid

ChemComp-AGG:
TIROFIBAN / medication, inhibitor*YM

ChemComp-I7R:
(4-{[(5S)-3-{4-[(E)-imino(4-methylpiperazin-1-yl)methyl]phenyl}-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid

ChemComp-IR7:
(4-{[2-oxo-4-(piperidin-4-yl)piperazin-1-yl]acetyl}phenoxy)acetic acid

ChemComp-MN:
Unknown entry

ChemComp-M6K:
(4-{[(5S)-3-(4-carbamimidoylphenyl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid

ChemComp-MJX:
{4-[4-(4-carbamimidoylphenyl)piperazin-1-yl]piperidin-1-yl}acetic acid

ChemComp-MV8:
(4-{[(5R)-3-(4-carbamimidoylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}piperazin-1-yl)acetic acid

ChemComp-MWI:
Lotrafiban

ChemComp-MWO:
(4-{[(5S)-3-(piperidin-4-yl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid

ChemComp-MAN:
alpha-D-mannopyranose

ChemComp-MWX:
Fradafiban

ChemComp-N9U:
Roxifiban

ChemComp-NB9:
Lamifiban

ChemComp-NJ9:
3-(4-{[(5S)-3-(4-carbamimidoylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}piperazin-1-yl)propanoic acid

ChemComp-NJF:
(1-{[(5S)-3-(4-carbamimidoylphenyl)-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperidin-4-yl)acetic acid

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
  • synthetic construct (others)
KeywordsCELL ADHESION / platelet aggregation / MEMBRANE PROTEIN-IMMUNE SYSTEM complex / integrin inhibitor / RGD mimetics / BLOOD CLOTTING/INHIBITOR / Complex / Inhibitor / BLOOD CLOTTING / BLOOD CLOTTING-INHIBITOR complex / CELL ADHESION/INHIBITOR / CELL ADHESION-INHIBITOR complex

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