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- PDB-3m6f: CD11A I-domain complexed with 6-((5S,9R)-9-(4-CYANOPHENYL)-3-(3,5... -

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Basic information

Entry
Database: PDB / ID: 3m6f
TitleCD11A I-domain complexed with 6-((5S,9R)-9-(4-CYANOPHENYL)-3-(3,5-DICHLOROPHENYL)-1-METHYL-2,4-DIOXO-1,3,7- TRIAZASPIRO[4.4]NON-7-YL)NICOTINIC ACID
ComponentsIntegrin alpha-L
KeywordsCELL ADHESION / LFA1 / INHIBITOR / Alternative splicing / Calcium / Disulfide bond / Glycoprotein / Integrin / Magnesium / Membrane / Polymorphism / Receptor / Transmembrane
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. ...Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BJZ / NITRATE ION / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSheriff, S.
Citation
Journal: J.Med.Chem. / Year: 2010
Title: Small molecule antagonist of leukocyte function associated antigen-1 (LFA-1): structure-activity relationships leading to the identification of 6-((5S,9R)-9-(4-cyanophenyl)-3-(3,5- ...Title: Small molecule antagonist of leukocyte function associated antigen-1 (LFA-1): structure-activity relationships leading to the identification of 6-((5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]nonan-7-yl)nicotinic acid (BMS-688521).
Authors: Watterson, S.H. / Xiao, Z. / Dodd, D.S. / Tortolani, D.R. / Vaccaro, W. / Potin, D. / Launay, M. / Stetsko, D.K. / Skala, S. / Davis, P.M. / Lee, D. / Yang, X. / McIntyre, K.W. / Balimane, P. ...Authors: Watterson, S.H. / Xiao, Z. / Dodd, D.S. / Tortolani, D.R. / Vaccaro, W. / Potin, D. / Launay, M. / Stetsko, D.K. / Skala, S. / Davis, P.M. / Lee, D. / Yang, X. / McIntyre, K.W. / Balimane, P. / Patel, K. / Yang, Z. / Marathe, P. / Kadiyala, P. / Tebben, A.J. / Sheriff, S. / Chang, C.Y. / Ziemba, T. / Zhang, H. / Chen, B.C. / DelMonte, A.J. / Aranibar, N. / McKinnon, M. / Barrish, J.C. / Suchard, S.J. / Murali Dhar, T.G.
#1: Journal: J.Med.Chem. / Year: 2006
Title: Discovery and Development of 5-[(5S,9R)-9-(4-Cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro [4.4]non-7-yl]methyl]-3-thiophenecarboxylicacid (BMS-587101) -- Small ...Title: Discovery and Development of 5-[(5S,9R)-9-(4-Cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro [4.4]non-7-yl]methyl]-3-thiophenecarboxylicacid (BMS-587101) -- Small Molecule Antagonist of LFA-1
Authors: Potin, D. / Launay, M. / Monatlik, F. / Malabre, P. / Fabreguettes, M. / Fouquet, A. / Maillet, M. / Nicolai, E. / Dorgeret, L. / Chevallier, F. / Besse, D. / Dufort, M. / Caussade, F. / ...Authors: Potin, D. / Launay, M. / Monatlik, F. / Malabre, P. / Fabreguettes, M. / Fouquet, A. / Maillet, M. / Nicolai, E. / Dorgeret, L. / Chevallier, F. / Besse, D. / Dufort, M. / Caussade, F. / Ahmad, S.Z. / Stetsko, D.K. / Skala, S. / Davis, P.M. / Balimane, P. / Patel, K. / Yang, Z. / Marathe, P. / Postelneck, J. / Townsend, R.M. / Sheriff, S. / Einspahr, H. / Kish, K. / Malley, M.F. / Gougoutas, J.Z. / Kadiyala, P. / Cheney, D.L. / Tejwani, R.W. / Murphy, D.K. / Mcintyre, K.W. / Yang, X. / Chao, S. / Leith, L. / Xiao, Z. / Mathur, A. / Chen, B.-C. / Wu, D.-R. / Traeger, S.C. / McKinnon, M. / Barrish, J.C. / Robl, J.A. / Iwanowicz, E.J. / Suchard, S.J. / Dhar, T.G.M.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.3Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5343
Polymers20,9361
Non-polymers5982
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.600, 63.600, 63.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain / CD11 antigen-like family member A


Mass: 20935.980 Da / Num. of mol.: 1 / Fragment: UNP residues 154-332
Source method: isolated from a genetically manipulated source
Details: REFOLDED FROM UREA MOL_ID: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P20701
#2: Chemical ChemComp-BJZ / 6-[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non-7-yl]pyridine-3-carboxylic acid


Mass: 536.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H19Cl2N5O4
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.78 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 12, 2003 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 13552 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 23
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.8 / % possible all: 76.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LFA

1lfa


Resolution: 1.85→28.4 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 1179626 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 685 5.1 %RANDOM
Rwork0.192 ---
obs0.193 13520 93.1 %-
all-13520 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.915 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 46.07 Å2 / Biso mean: 17.851 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--2.02 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.85→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 41 101 1593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.85→1.93 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 69 4.9 %
Rwork0.214 1339 -
all-1408 -
obs--78.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMCOMBINED.TOP
X-RAY DIFFRACTION5BJZ.PARBJZ.TOP

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