4YZU: Coagulation factor IX

Rapid development of two Factor IXa inhibitors from Hit to Lead. Determined by X-ray diffraction at 1.41 Å resolution. Released 20 May 2015.

Method: X-ray diffraction
Resolution: 1.41 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,696
Mol. weight: 33.57 kDa
Ligands: NHE, 4K6
Released: 20 May 2015

Explore 4YZU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YZU contains 10 α-helices and 28 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, 24 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	42-48	7	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	65-68	4	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	95	1	5
β-strand	97	1	5
β-strand	104-108	5	3
β-strand	115	1	6
β-strand	118	1	6
α-helix	120-121	2
β-strand	122	1	2
α-helix	126-132	9
β-strand	135-140	6	2
β-strand	143	1	7
α-helix	150	1
β-strand	151	1	7
α-helix	152	1
β-strand	154	1	4
β-strand	156-162	7	2
α-helix	165-170	6
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	235-242	8

Chain B: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	91-94	4
β-strand	98-102	5	8
β-strand	106-110	5	8
β-strand	115-117	3	9
β-strand	124-126	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor IX	A	protein	235	Homo sapiens	P00740 (AlphaFold model)
Coagulation factor IX	B	protein	62	Homo sapiens	P00740 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YZU_1 Coagulation factor IX (chains A)
VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEE
TEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFL
KFGSGYVSGWGRVFHKGASALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDS
CQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

Sequence of entity 2 (B), FASTA

>4YZU_2 Coagulation factor IX (chains B)
MDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKL
TR

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	1
4K6	N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzami…	C20 H20 N6 O	1

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

Primary citation

Rapid development of two factor IXa inhibitors from hit to lead. Parker, D.L., Walsh, S., Li, B. et al. Bioorg Med Chem Lett (2015) 25:2321-2325. DOI 10.1016/j.bmcl.2015.04.025 · PubMed

Other PDB entries of the same protein (UniProt P00740 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JB9 1.3 Å, Crystal structure of factor IXa K98T variant in complex with PPACK
6MV4 1.37 Å, Crystal structure of human coagulation factor ixa
5JBA 1.4 Å, Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK
5TNT 1.4 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
4Z0K 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
5JB8 1.45 Å, Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone
1EDM 1.5 Å, Epidermal growth factor-like domain from human factor IX
2WPH 1.5 Å, factor IXa superactive triple mutant
5TNO 1.54 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
5JBB 1.56 Å, Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with…
2WPJ 1.6 Å, factor IXa superactive triple mutant, NaCl-soaked
6RFK 1.6 Å, Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)

Browse structure collections

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