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Orally active thrombin inhibitors in complex with thrombin and an exosite decapeptide

Analyse Orally active thrombin inhibitors in complex with thrombin and an exosite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ANK
Type: protein
Length: 294 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin heavy chain; Thrombin light chain; Synthetic peptide
EC: 3.4.21.5
UniProt: P00734
Ligands: N12
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Thrombin heavy chain (EC 3.4.21.5)	protein	250	14% helix, 35% strand	P00734
L	Thrombin light chain	protein	34	26% helix, 0% strand	P00734
P	Synthetic peptide	protein	10	30% helix, 0% strand	—

Ligands and binding sites

N12 · N-[(1R)-2-[(1-{[({6-[amino(imino)methyl]pyridin-3-yl}methyl)amino]carbonyl}cyclopentyl)amino]-1-(cyclohexylmethyl)-2-oxoethyl]glycine · ligand · chains H
SIN · Succinic acid · additive · chains H, P

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	275	0.55	0.76	36	N12
2	63	0.33	0.76	20	empty
3	50	0.31	0.77	14	empty

Interfaces

2 interfaces between chains.

H–L · 1401 Å² buried · 33 hydrogen bonds · protein-protein
H–P · 707 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 modified, 1 covalent (disulfide, nonstandard, additive adduct, hydroxylation).

Compared structures

2ANK · orally active thrombin inhibitors in complex with thrombin and an exosite decapeptide · the same entry in another collection · chain H against H, TM-score 1.00

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 P00734
Elsewhere: RCSB PDB 2ANK · PDBe 2ANK · UniProt P00734

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