6TS6: Coagulation factor XI protease domain

Coagulation factor XI protease domain in complex with active site inhibitor. Determined by X-ray diffraction at 1.33 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,201
Mol. weight: 27.82 kDa
Ligands: NW5
Released: 8 Jul 2020

Explore 6TS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TS6 contains 10 α-helices and 21 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: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
β-strand	30-35	6	3
β-strand	37D-46	10	3
β-strand	51-54	4	3
α-helix	56-59	4
α-helix	62-64	3
β-strand	65-68	4	3
β-strand	73	1	4
α-helix	74-76	3
β-strand	83-90	8	3
α-helix	97-99	3
β-strand	104-108	5	3
α-helix	111-114	4
β-strand	115	1	5
β-strand	118	1	5
β-strand	123	1	2
α-helix	124-126	3
β-strand	136-140	5	2
β-strand	154	1	4
α-helix	155	1
β-strand	156-159	4	2
β-strand	162-163	2	2
α-helix	165-171	7
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-202A	6	2
β-strand	202D-215	10	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor XI	A	protein	238	Homo sapiens	P03951 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6TS6_1 Coagulation factor XI (chains A)
IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSG
ILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDR
NVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGG
KDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV

Ligands and cofactors

ID	Name	Formula	Copies
NW5	2-[2-[[3-[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-5-yl]-5-(2-cyanopropan-2-yl…	C27 H26 N2 O4	1

Water and common crystallization additives (SO4, DMS) are not listed.

Primary citation

Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach. Lorthiois, E., Roache, J., Barnes-Seeman, D. et al. J Med Chem (2020) 63:8088-8113. DOI 10.1021/acs.jmedchem.0c00279 · PubMed

Other PDB entries of the same protein (UniProt P03951 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MBO 0.92 Å, FACTOR XIA (PICHIA PASTORIS; C500S [C122S]) IN COMPLEX WITH THE INHIBITOR Milvexian…
6TS4 1.17 Å, Coagulation factor XI protease domain in complex with active site inhibitor
4CRG 1.25 Å, Creating novel F1 inhibitors through fragment based lead generation and structure aided…
8BO6 1.25 Å, Coagulation factor XI protease domain in complex with active site inhibitor 2
8BO7 1.25 Å, Coagulation factor XI protease domain in complex with active site inhibitor 34
6USY 1.26 Å, Coagulation factor XI catalytic domain (C123S) in complex with nvp-XIV936
6TS5 1.29 Å, Coagulation factor XI protease domain in complex with active site inhibitor
7V11 1.47 Å, Factor XIa in Complex with Compound 2e
5EXN 1.49 Å, FACTOR XIA (C500S [C122S]) IN COMPLEX WITH THE INHIBITOR methyl…
7V16 1.5 Å, Factor XIa in Complex with Compound 2j
7V17 1.52 Å, Factor XIa in Complex with Compound 2k
5TKS 1.55 Å, Factor xia in complex with the inhibitor ((15S)-18-chloro-…

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