2VWN: Aminopyrrolidine Factor Xa inhibitor

Aminopyrrolidine Factor Xa inhibitor. Determined by X-ray diffraction at 1.61 Å resolution. Released 7 Jul 2009.

Method: X-ray diffraction
Resolution: 1.61 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,523
Mol. weight: 33.88 kDa
Ligands: CA, H25
Released: 7 Jul 2009

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

Secondary structure: helices and β-sheets

2VWN contains 13 α-helices and 27 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	40-46	7	3
β-strand	51-54	4	3
α-helix	56-60	5
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-83	3	3
β-strand	85-90	6	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	92-95	4
β-strand	99-101	3	7
β-strand	108-110	3	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

>2VWN_1 ACTIVATED FACTOR XA HEAVY CHAIN (chains A)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGEQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKA
K

Sequence of entity 2 (L), FASTA

>2VWN_2 FACTOR X LIGHT CHAIN (chains L)
RKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
H25	5-Chloro-thiophene-2-carboxylic acid ((3S,4S)-1-{[2-fluoro-4-(2-oxo-2H-pyridin-…	C22 H20 Cl F N4 O4 S	1

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

Primary citation

Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit. Zbinden, K.G., Anselm, L., Banner, D.W. et al. Eur J Med Chem (2009) 44:2787. DOI 10.1016/J.EJMECH.2008.12.025 · 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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