7M3Z: TIM-3

Structure of TIM-3 in complex with N-(4-(8-chloro-2-mehtyl-5-oxo-5,6-dihydro-[1,2,4]triazolo[1,5-c]quinazolin-9-yl)-3-methylphenyl)methanesulfonamdide (compound 35). Determined by X-ray diffraction at 1.4 Å resolution. Released 13 Oct 2021.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,030
Mol. weight: 12.76 kDa
Ligands: YQD, CA
Released: 13 Oct 2021

Explore 7M3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M3Z contains 3 α-helices and 11 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
α-helix	12	1
β-strand	13-15	3	2
β-strand	18	1	3
β-strand	30-34	5	1
β-strand	44-49	6	1
β-strand	54-57	4	1
β-strand	61-62	2	2
α-helix	67-69	3
β-strand	71	1	3
β-strand	74-76	3	2
α-helix	81-83	3
β-strand	85-91	7	1
β-strand	100-108	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hepatitis A virus cellular receptor 2	A	protein	109	Homo sapiens	Q8TDQ0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M3Z_1 Hepatitis A virus cellular receptor 2 (chains A)
SEVEYRAEVGQNAYLPCFYTPAAPGNLVPVCWGKGACPVFECGNVVLRTDERDVNYWTSR
YWLNGDFRKGDVSLTIENVTLADSGIYCCRIQIPGIMNDEKFNLKLVIK

Ligands and cofactors

ID	Name	Formula	Copies
YQD	N-{4-[(4S,10aP)-8-chloro-2-methyl-5-oxo-5,6-dihydro[1,2,4]triazolo[1,5-c]quinaz…	C18 H16 Cl N5 O3 S	1
CA	Calcium ion	Ca	1

Primary citation

Fragment-Based Discovery of Small Molecules Bound to T-Cell Immunoglobulin and Mucin Domain-Containing Molecule 3 (TIM-3). Rietz, T.A., Teuscher, K.B., Mills, J.J. et al. J Med Chem (2021) 64:14757-14772. DOI 10.1021/acs.jmedchem.1c01336 · PubMed

Other PDB entries of the same protein (UniProt Q8TDQ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KQL 1.49 Å, Anti-Tim3 antibody Fab complex
7M3Y 1.69 Å, Structure of TIM-3 in complex with 8-chloro-2-methyl-9-(3-mehtylpyridin-4-yl)-[1,2,4]tria…
6DHB 1.7 Å, Crystal structure of the human TIM-3 with bound Calcium
7M41 1.79 Å, Structure of TIM-3 in complex with N-(4-(8-chloro-2-methyl-5-oxo-5,6-dihydro-[1,2,4]traiz…
8TFT 2.3 Å, Fab of O13-1 human IgG1 antibody bound to IgV domain of human TIM-3
5F71 2.4 Å, Human T-cell immunoglobulin and mucin domain protein 3 (hTIM-3)
8TBB 2.5 Å, F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3
6TXZ 3.06 Å, FAB part of M6903 in complex with human TIM3
5DZL 3.4 Å, Crystal structure of the protein human CEACAM1
8HGJ 4.82 Å, Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3)…

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