8BO6: Coagulation factor XI protease domain

Coagulation factor XI protease domain in complex with active site inhibitor 2. Determined by X-ray diffraction at 1.25 Å resolution. Released 13 Sept 2023.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,300
Mol. weight: 27.91 kDa
Ligands: CIT, QW0
Released: 13 Sept 2023

Explore 8BO6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BO6 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 AAA: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	389	1	1
β-strand	392-393	2	2
β-strand	402-407	6	3
β-strand	413-422	10	3
β-strand	425-428	4	3
α-helix	430-433	4
α-helix	439-441	3
β-strand	442-446	5	3
β-strand	450	1	4
α-helix	451-453	3
β-strand	461	1	3
β-strand	463-468	6	3
α-helix	475-477	3
β-strand	482-486	5	3
α-helix	489-492	4
β-strand	493	1	5
β-strand	496	1	5
β-strand	500	1	2
α-helix	501-503	3
β-strand	514-518	5	2
β-strand	531	1	4
β-strand	533-536	4	2
β-strand	539-540	2	2
α-helix	542-548	7
β-strand	558-561	4	2
β-strand	569	1	1
β-strand	578-583	6	2
β-strand	586-595	10	2
β-strand	606-610	5	2
α-helix	611-614	4
α-helix	615-623	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor XIa light chain	AAA	protein	238	Homo sapiens	P03951 (AlphaFold model)

Sequence of entity 1 (AAA), FASTA

>8BO6_1 Coagulation factor XIa light chain (chains AAA)
IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSG
ILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDR
NVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGG
KDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
QW0	(~{E})-~{N}-[[5-(3-azanyl-1~{H}-indazol-6-yl)-4-chloranyl-1~{H}-imidazol-2-yl]m…	C21 H16 Cl2 N10 O	1

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

Primary citation

Design and Preclinical Characterization Program toward Asundexian (BAY 2433334), an Oral Factor XIa Inhibitor for the Prevention and Treatment of Thromboembolic Disorders. Roehrig, S., Ackerstaff, J., Jimenez Nunez, E. et al. J Med Chem (2023) 66:12203-12224. DOI 10.1021/acs.jmedchem.3c00795 · 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…
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
6TS6 1.33 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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