3M6F: CD11A I-domain

CD11A 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. Determined by X-ray diffraction at 1.85 Å resolution. Released 12 May 2010.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,595
Mol. weight: 21.53 kDa
Ligands: BJZ
Released: 12 May 2010

Explore 3M6F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M6F contains 12 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	130-137	8	1
β-strand	139	1	2
α-helix	144-160	17
β-strand	166-173	8	1
β-strand	177-181	5	1
α-helix	183-189	7
α-helix	192-195	4
β-strand	204	1	2
α-helix	208-214	7
α-helix	215-219	5
α-helix	222-224	3
β-strand	231-238	8	1
α-helix	249-251	3
β-strand	255-261	7	1
α-helix	263-265	3
α-helix	268-271	4
α-helix	272-277	6
α-helix	282-285	4
β-strand	286-289	4	1
α-helix	294-304	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-L	A	protein	183	Homo sapiens	P20701 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3M6F_1 Integrin alpha-L (chains A)
GSHMNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFS
DYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATD
SGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQK
KIY

Ligands and cofactors

ID	Name	Formula	Copies
BJZ	6-[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-tr…	C26 H19 Cl2 N5 O4	1

Water and common crystallization additives (NO3) are not listed.

Primary citation

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). Watterson, S.H., Xiao, Z., Dodd, D.S. et al. J Med Chem (2010) 53:3814-3830. DOI 10.1021/jm100348u · PubMed

Other PDB entries of the same protein (UniProt P20701 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MJN 1.3 Å, Crystal Structure of the intermediate affinity aL I domain mutant
2ICA 1.56 Å, CD11a (LFA1) I-domain complexed with BMS-587101 aka 5-[(5S,…
3F78 1.6 Å, Crystal structure of wild type LFA1 I domain complexed with isoflurane
1T0P 1.66 Å, Structural Basis of ICAM recognition by integrin alpahLbeta2 revealed in the complex…
3F74 1.7 Å, Crystal structure of wild type LFA1 I domain
2O7N 1.75 Å, CD11A (LFA1) I-domain complexed with 7A-[(4-cyanophenyl)methyl]-6-(3,5-dichlorophenyl)-5-…
1LFA 1.8 Å, CD11A I-domain with bound MN++
1XUO 1.8 Å, X-ray structure of LFA-1 I-domain bound to a 1,4-diazepane-2,5-dione inhibitor at 1.8A…
3BQN 1.8 Å, LFA-1 I domain bound to inhibitors
4IXD 1.8 Å, X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a resolution
7KC3 1.8 Å, X-ray structure of Lfa-1 I domain collected at 273 K
7KC6 1.85 Å, X-ray structure of Lfa-1 I domain in complex with Lovastatin collected at 273 K

Browse structure collections

About this viewer

MolViewer shows 3M6F directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.