2XBV: Factor Xa

Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor. Determined by X-ray diffraction at 1.66 Å resolution. Released 4 Aug 2010.

Method: X-ray diffraction
Resolution: 1.66 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,483
Mol. weight: 33.82 kDa
Ligands: XBV, CA
Released: 4 Aug 2010

Explore 2XBV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XBV contains 13 α-helices and 26 β-strands across 2 chains. 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, 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	30-34	5	3
β-strand	40-46	7	3
β-strand	51-54	4	3
α-helix	56-60	5
β-strand	65-68	4	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	104-108	5	3
β-strand	115	1	5
β-strand	118	1	5
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-124A	3
α-helix	125-127	3
α-helix	128-131A	5
β-strand	135-140	6	2
β-strand	143	1	6
α-helix	150	1
β-strand	151	1	6
α-helix	152	1
β-strand	154	1	4
β-strand	156-163	8	2
α-helix	165-171	7
α-helix	175-177	3
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-241	7

Chain L: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	93-95	3
β-strand	99	1	7
β-strand	110	1	7
β-strand	115-117	3	8
β-strand	124-126	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated factor xa heavy chain	A	protein	241	HOMO SAPIENS	P00742 (AlphaFold model)
Factor X light chain	L	protein	55	HOMO SAPIENS	P00742 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2XBV_1 ACTIVATED FACTOR XA HEAVY CHAIN (chains A)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGEQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKA
K

Sequence of entity 2 (L), FASTA

>2XBV_2 FACTOR X LIGHT CHAIN (chains L)
RKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERR

Ligands and cofactors

ID	Name	Formula	Copies
XBV	(3R,4R)-1-(2,2-difluoro-ethyl)-pyrrolidine-3,4-dicarboxylic acid…	C24 H21 Cl F3 N5 O3	1
CA	Calcium ion	Ca	1

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

Primary citation

Discovery of a Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} as a Clinical Candidate. Anselm, L., Banner, D.W., Benz, J. et al. Bioorg Med Chem (2010) 20:5313. DOI 10.1016/J.BMCL.2010.06.126 · PubMed

Other PDB entries of the same protein (UniProt P00742 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I24 1.2 Å, Coagulation factor Xa complex with a2-loop peptide
2JKH 1.25 Å, Factor Xa - cation inhibitor complex
2Y5F 1.29 Å, Factor xa - cation inhibitor complex
2Y5G 1.29 Å, Factor xa - cation inhibitor complex
2Y5H 1.33 Å, Factor xa - cation inhibitor complex
3KL6 1.45 Å, Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and…
2PR3 1.5 Å, Factor XA inhibitor
6YYX 1.53 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
3FFG 1.54 Å, Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPH…
7YB9 1.54 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
4Y6D 1.55 Å, Factor Xa complex with GTC000101
2VWO 1.6 Å, Aminopyrrolidine Factor Xa inhibitor

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