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Rapid development of two factor ixa inhibitors from hit to lead

Analyse Rapid development of two factor ixa inhibitors from hit to lead in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z0K
Type: protein
Length: 289 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor IX
EC: 3.4.21.22
UniProt: P00740
Ligands: 4LN, NA, CL
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor IX (EC 3.4.21.22)	protein	234	13% helix, 37% strand	P00740
B	Coagulation factor IX (EC 3.4.21.22)	protein	55	7% helix, 25% strand	P00740

Ligands and binding sites

4LN · N-[(2R)-10-hydroxy-2,7-dimethyl-1,2,3,4-tetrahydropyrido[1,2-b]indazol-2-yl]-4-(4H-1,2,4-triazol-4-yl)benzamide · ligand · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · chains B
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	175	0.48	0.76	21	empty
2	101	0.46	0.80	25	4LN
3	53	0.33	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 815 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

4Z0K · Rapid development of two Factor IXa inhibitors from Hit to Lead · the same entry in another collection · chain A against A, TM-score 1.00
P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00740
Elsewhere: RCSB PDB 4Z0K · PDBe 4Z0K · UniProt P00740

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