2ICA - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CD11A (LFA1) I-DOMAIN COMPLEXED WITH BMS-587101 AKA 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

Authors :   S. Sheriff, H. Einspahr

Date :   12 Sep 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.56

Chains :   Asym./Biol. Unit : A

Keywords :   Inhibitor, Protein/Ligand Complex, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Potin, M. Launay, F. Monatlik, P. Malabre, M. Fabreguettes, A. Fouquet, M. Maillet, E. Nicolai, L. Dorgeret, F. Chevallier, D. Besse, M. Dufort, F. Caussade, S. Z. Ahmad, D. K. Stetsko, S. Skala, P. M. Davis, P. Balimane, K. Patel, Z. Yang, P. Marathe, J. Postelneck, R. M. Townsend, V. Goldfarb, S. Sheriff, H. Einspahr, K. Kish, M. F. Malley, J. D. Dimarco, J. Z. Gougoutas, P. Kadiyala, D. L. Cheney, R. W. Tejwani, D. K. Murphy, K. W. Mcintyre, X. Yang, S. Chao, L. Leith, Z. Xiao, A. Mathur, B. C. Chen, D. R. Wu, S. C. Traeger, M. Mckinnon, J. C. Barrish, J. A. Robl, E. J. Iwanowicz, S. J. Suchard, T. G. Dhar
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-Thiophenecarboxylic Acid (Bms-587101)-A Small Molecule Antagonist Leukocyte Function Associated Antigen-1.
J. Med. Chem. V. 49 6946 2006
PubMed-ID: 17125246 | Reference-DOI: 10.1021/JM0610806
(for further references see the PDB file header)

Molecule 1 - INTEGRIN ALPHA-L
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	VWFA DOMAIN, RESIDUES 154-332
	Gene	:	ITGAL, CD11A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MINIMAL MEDIA
	Synonym	:	LEUKOCYTE ADHESION GLYCOPROTEIN LFA-1 ALPHA CHAIN, LFA-1A, LEUKOCYTE FUNCTION-ASSOCIATED MOLECULE 1 ALPHA CHAIN, CD11A ANTIGEN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	2IC	1	Ligand/Ion	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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:166 , VAL A:233 , ILE A:235 , ILE A:255 , TYR A:257 , ILE A:259 , LYS A:287 , LEU A:302 , ILE A:306 , HOH A:324 , HOH A:381	BINDING SITE FOR RESIDUE 2IC A 1

(no "SS Bond" information available for 2ICA)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:280	-	Pro A:281

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025236	R	214	W	ITAL_HUMAN	Polymorphism	1064524	A	R	189	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VWFA	PS50234	VWFA domain profile.	ITAL_HUMAN	156-327	1	A:131-302

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000356798	1a	ENSE00002147085	chr16:30483983-30484219	237	ITAL_HUMAN	1-21	21	0	-	-
1.2b	ENST00000356798	2b	ENSE00001770886	chr16:30485517-30485619	103	ITAL_HUMAN	21-55	35	0	-	-
1.3	ENST00000356798	3	ENSE00001621476	chr16:30486627-30486721	95	ITAL_HUMAN	55-87	33	0	-	-
1.4	ENST00000356798	4	ENSE00001775052	chr16:30486834-30486901	68	ITAL_HUMAN	87-109	23	0	-	-
1.5	ENST00000356798	5	ENSE00001718084	chr16:30490412-30490529	118	ITAL_HUMAN	110-149	40	0	-	-
1.6	ENST00000356798	6	ENSE00001643987	chr16:30490652-30490782	131	ITAL_HUMAN	149-192	44	1	A:128-167	40
1.7	ENST00000356798	7	ENSE00001594214	chr16:30492760-30492905	146	ITAL_HUMAN	193-241	49	1	A:168-216	49
1.8	ENST00000356798	8	ENSE00001756914	chr16:30495148-30495280	133	ITAL_HUMAN	241-285	45	1	A:216-260	45
1.9	ENST00000356798	9	ENSE00001781646	chr16:30495434-30495584	151	ITAL_HUMAN	286-336	51	1	A:261-306	46
1.10	ENST00000356798	10	ENSE00001704215	chr16:30500403-30500476	74	ITAL_HUMAN	336-360	25	0	-	-
1.11	ENST00000356798	11	ENSE00001741327	chr16:30500575-30500707	133	ITAL_HUMAN	361-405	45	0	-	-
1.12	ENST00000356798	12	ENSE00001592674	chr16:30505533-30505684	152	ITAL_HUMAN	405-455	51	0	-	-
1.13	ENST00000356798	13	ENSE00001785598	chr16:30506034-30506171	138	ITAL_HUMAN	456-501	46	0	-	-
1.14	ENST00000356798	14	ENSE00001694693	chr16:30507418-30507615	198	ITAL_HUMAN	502-567	66	0	-	-
1.15	ENST00000356798	15	ENSE00001704204	chr16:30507757-30507887	131	ITAL_HUMAN	568-611	44	0	-	-
1.16a	ENST00000356798	16a	ENSE00001611961	chr16:30510395-30510555	161	ITAL_HUMAN	611-665	55	0	-	-
1.17	ENST00000356798	17	ENSE00001610939	chr16:30510659-30510810	152	ITAL_HUMAN	665-715	51	0	-	-
1.18	ENST00000356798	18	ENSE00001693046	chr16:30515496-30515585	90	ITAL_HUMAN	716-745	30	0	-	-
1.19a	ENST00000356798	19a	ENSE00001609957	chr16:30516565-30516621	57	ITAL_HUMAN	746-764	19	0	-	-
1.20	ENST00000356798	20	ENSE00001755479	chr16:30516710-30516783	74	ITAL_HUMAN	765-789	25	0	-	-
1.21	ENST00000356798	21	ENSE00001735592	chr16:30518036-30518177	142	ITAL_HUMAN	789-836	48	0	-	-
1.22	ENST00000356798	22	ENSE00001788360	chr16:30521682-30521792	111	ITAL_HUMAN	837-873	37	0	-	-
1.23a	ENST00000356798	23a	ENSE00001758712	chr16:30522202-30522281	80	ITAL_HUMAN	874-900	27	0	-	-
1.24	ENST00000356798	24	ENSE00001615572	chr16:30522371-30522457	87	ITAL_HUMAN	900-929	30	0	-	-
1.25	ENST00000356798	25	ENSE00001670842	chr16:30525092-30525167	76	ITAL_HUMAN	929-954	26	0	-	-
1.26	ENST00000356798	26	ENSE00001795073	chr16:30528294-30528407	114	ITAL_HUMAN	955-992	38	0	-	-
1.27	ENST00000356798	27	ENSE00001688272	chr16:30528970-30529026	57	ITAL_HUMAN	993-1011	19	0	-	-
1.28	ENST00000356798	28	ENSE00001734661	chr16:30529118-30529216	99	ITAL_HUMAN	1012-1044	33	0	-	-
1.29	ENST00000356798	29	ENSE00001721322	chr16:30529945-30530040	96	ITAL_HUMAN	1045-1076	32	0	-	-
1.30	ENST00000356798	30	ENSE00001673761	chr16:30531178-30531288	111	ITAL_HUMAN	1077-1113	37	0	-	-
1.31b	ENST00000356798	31b	ENSE00001399855	chr16:30532813-30534505	1693	ITAL_HUMAN	1114-1170	57	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:179
 aligned with ITAL_HUMAN | P20701 from UniProtKB/Swiss-Prot  Length:1170

    Alignment length:179
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322         
           ITAL_HUMAN   153 GNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKI 331
               SCOP domains d2icaa_ A: Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1)                                                                                                     SCOP domains
               CATH domains 2icaA00 A:128-306  [code=3.40.50.410, no name defined]                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeehhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhh.....eeeeeeee.........hhhhh..eeeeeee.hhhhhhhhhhhhhhhh..hhhhheeee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------W--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VWFA  PDB: A:131-302 UniProt: 156-327                                                                                                                                       ---- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:128-167 [INCOMPLETE]   Exon 1.7  PDB: A:168-216 UniProt: 193-241        --------------------------------------------Exon 1.9  PDB: A:261-306 UniProt: 286-336      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.8  PDB: A:216-260 UniProt: 241-285    ---------------------------------------------- Transcript 1 (2)
                 2ica A 128 MNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKI 306
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: vWA-like (111)

Superfamily: vWA-like (111)

Family: Integrin A (or I) domain (84)

Protein domain: Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1) (26)

Human (Homo sapiens) [TaxId: 9606] (26)

d2icaa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.410, no name defined] (87)

Human (Homo sapiens) (66)

2icaA00

A:128-306

(no "Pfam Domain" information available for 2ICA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ITAL_HUMAN | P20701)

molecular function
	GO:0030369	ICAM-3 receptor activity	Combining with ICAM-3, intercellular adhesion molecule 3, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. ICAM-3, or CD50, are constitutively expressed on monocytes, granulocytes and lymphocytes; on physiological stimulation, they become transiently phosphorylated on serine residues.
	GO:0050839	cell adhesion molecule binding	Interacting selectively and non-covalently with a cell adhesion molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0002291	T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	The change in morphology and behavior of a mature or immature T cell resulting from exposure to an antigen for which its T cell receptor is specific bound to an MHC molecule on an antigen presenting cell, leading to the initiation or perpetuation of an immune response.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0007157	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0007229	integrin-mediated signaling pathway	A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007159	leukocyte cell-cell adhesion	The attachment of a leukocyte to another cell via adhesion molecules.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0006928	movement of cell or subcellular component	The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
	GO:0043113	receptor clustering	The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0016337	single organismal cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0034687	integrin alphaL-beta2 complex	An integrin complex that comprises one alphaL subunit and one beta2 subunit.
	GO:0008305	integrin complex	A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		2IC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:280 - Pro A:281	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2ica
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ITAL_HUMAN \| P20701
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ITAL_HUMAN \| P20701
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2ICA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (27, 27)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File