6T9T: Matriptase

Matriptase in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904). Determined by X-ray diffraction at 1.69 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,159
Mol. weight: 27.14 kDa
Ligands: MXH
Released: 18 Nov 2020

Explore 6T9T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T9T contains 9 α-helices and 22 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	51-54	4	3
α-helix	56-59	4
β-strand	60B	1	4
β-strand	60E	1	4
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-90	10	3
β-strand	104-108	5	3
β-strand	122	1	2
α-helix	123-125	3
β-strand	135-140	6	2
β-strand	143	1	6
β-strand	151	1	6
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-184	5	2
β-strand	189	1	1
α-helix	197	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of tumorigenicity 14 protein	A	protein	241	Homo sapiens	Q9Y5Y6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6T9T_1 Suppressor of tumorigenicity 14 protein (chains A)
VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTA
FLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPD
ASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFL
SGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTG
V

Ligands and cofactors

ID	Name	Formula	Copies
MXH	1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-[3-fluoranyl-4-(h…	C33 H41 F N6 O5 S	1

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

Primary citation

Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors. Pilgram, O., Keils, A., Benary, G.E. et al. Eur J Med Chem (2022):114437. DOI 10.1016/j.ejmech.2022.114437

Other PDB entries of the same protein (UniProt Q9Y5Y6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NCL 1.19 Å, Crystal Structure of MT-SP1 bound to Benzamidine Phosphonate Inhibitor
3P8G 1.2 Å, Crystal Structure of MT-SP1 in complex with benzamidine
8G1W 1.2 Å, Crystal Structure Matriptase (C731S) in Complex with Inhibitor VD4162B
1EAX 1.3 Å, Crystal structure of MTSP1 (matriptase)
8G1V 1.35 Å, Crystal Structure Matriptase (C731S) in Complex with Inhibitor MM1132-2
4IS5 1.48 Å, Crystal Structure of the ligand-free inactive Matriptase
3NPS 1.5 Å, Crystal structure of membrane-type serine protease 1 (MT-SP1) in complex with the Fab…
4JZ1 1.9 Å, Crystal Structure of Matriptase in complex with Inhibitor
4O9V 1.9 Å, Crystal structure of matriptase in complex with inhibitor
4R0I 1.9 Å, Crystal structure of matriptase in complex with inhibitor
6N4T 1.95 Å, Crystal structure of Matriptase1 in complex with a peptidomimetic benzothiazole
3P8F 2.0 Å, Crystal Structure of MT-SP1 in complex with SFTI-1

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