3CEN: Factor XA

Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl) amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)benzamide. Determined by X-ray diffraction at 1.6 Å resolution. Released 20 May 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,550
Mol. weight: 32.52 kDa
Ligands: FXA
Released: 20 May 2008

Explore 3CEN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CEN 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	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	156-162	7	2
α-helix	163-164	2
α-helix	165-171	7
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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	88-90	3
α-helix	92-95	4
β-strand	99-102	4	7
β-strand	107-110	4	7
β-strand	115-117	3	8
β-strand	124-126	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor X, heavy chain	A	protein	234	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor X, light chain	L	protein	52	Homo sapiens	P00742 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3CEN_1 COAGULATION FACTOR X, HEAVY CHAIN (chains A)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT

Sequence of entity 2 (L), FASTA

>3CEN_2 COAGULATION FACTOR X, LIGHT CHAIN (chains L)
KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE

Ligands and cofactors

ID	Name	Formula	Copies
FXA	N-(2-(((5-chloro-2-pyridinyl)amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)be…	C23 H17 Cl N4 O4 S	1

Primary citation

Structure-Activity Relationships of Anthranilamide-Based Factor Xa Inhibitors Containing Piperidinone and Pyridinone P4 Moieties. Corte, J.R., Fang, T., Pinto, D.J.P. et al. Bioorg Med Chem Lett (2008) 18:2845-2849. DOI 10.1016/j.bmcl.2008.03.092 · 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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