2PR3: Factor XA inhibitor

Factor XA inhibitor. Determined by X-ray diffraction at 1.5 Å resolution. Released 14 Aug 2007.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,482
Mol. weight: 32.53 kDa
Ligands: CA, 237
Released: 14 Aug 2007

Explore 2PR3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PR3 contains 10 α-helices and 24 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: 9 helices, 20 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	56-61	6
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	1
α-helix	125-127	3
α-helix	128-131B	5
β-strand	135-140	6	2
β-strand	154	1	4
β-strand	156-162	7	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 B: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	11-15	5	6
β-strand	18-22	5	6
β-strand	27-29	3	7
β-strand	36-38	3	7

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	B	protein	51	Homo sapiens	P00742 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PR3_1 COAGULATION FACTOR X, HEAVY CHAIN (chains A)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT

Sequence of entity 2 (B), FASTA

>2PR3_2 COAGULATION FACTOR X, LIGHT CHAIN (chains B)
LCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
237	(2R,4R)-N~1~-(4-chlorophenyl)-N~2~-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-…	C26 H25 Cl F N3 O5 S	1

Primary citation

Structure-based drug design of pyrrolidine-1, 2-dicarboxamides as a novel series of orally bioavailable factor Xa inhibitors. Van Huis, C.A., Bigge, C.F., Casimiro-Garcia, A. et al. Chem Biol Drug Des (2007) 69:444-450. DOI 10.1111/j.1747-0285.2007.00520.x · 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…
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
3CEN 1.6 Å, Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl)…

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