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Cathepsin L with AZ13010160

Analyse Cathepsin L with AZ13010160 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HWN
Type: protein
Length: 862 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin L1
EC: 3.4.22.15
UniProt: P07711
Ligands: BD3
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin L1 (EC 3.4.22.15)	protein	213	31% helix, 21% strand	P07711
B	Cathepsin L1 (EC 3.4.22.15)	protein	215	29% helix, 22% strand	P07711
C	Cathepsin L1 (EC 3.4.22.15)	protein	220	29% helix, 23% strand	P07711
D	Cathepsin L1 (EC 3.4.22.15)	protein	214	28% helix, 23% strand	P07711

Ligands and binding sites

BD3 · Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-L-phenylalaninamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1013	0.79	0.81	107	empty
2	178	0.51	0.78	31	empty
3	86	0.45	0.80	18	empty
4	120	0.36	0.73	21	empty
5	98	0.33	0.73	24	empty

Interfaces

4 interfaces between chains.

A–C · 567 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 426 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 351 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 276 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

3HWN · CATHEPSIN L with AZ13010160 · the same entry in another collection · chain D against D, TM-score 1.00
P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain B against A, 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 P07711
Elsewhere: RCSB PDB 3HWN · PDBe 3HWN · UniProt P07711

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