Research workbench

Benzothiophene inhibitors of factor ixa

Analyse Benzothiophene inhibitors of factor ixa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LC3
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor IX
EC: 3.4.21.22
UniProt: P00740
Ligands: IYX, CA
Pockets: 4 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Coagulation factor IX (EC 3.4.21.22)	protein	235	12% helix, 36% strand	P00740
B, D	Coagulation factor IX (EC 3.4.21.22)	protein	57	7% helix, 21% strand	P00740

Ligands and binding sites

IYX · 1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine · ligand · 4 copies · chains A, C
CA · Calcium ion · metal · 2 copies · chains A, C

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

Pockets

4 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	161	0.49	0.77	29	empty
2	160	0.49	0.77	21	empty
3	115	0.41	0.76	29	IYX
4	100	0.41	0.77	23	IYX

Interfaces

3 interfaces between chains.

C–D · 850 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 848 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 65 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

3LC3 · Benzothiophene Inhibitors of Factor IXa · the same entry in another collection · chain D against D, TM-score 1.00
P00740 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P00740) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 3LC3 · PDBe 3LC3 · UniProt P00740

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.