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MolNFT v1 · #161465 · protein

Crystal structure of human kallikrein 5 in complex with GSK144

6QFE · Kallikrein-5: “Crystal structure of human kallikrein 5 in complex with GSK144”. X-ray diffraction, 3 ligands (J08, NAG, NA), 1 pocket (best druggability 0.78). MolNFT v1 #161465 on GenesisL1: 3D structure, binding sites and pockets…

PDB
6QFE
Type
protein
Length
454 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Kallikrein-5
EC
3.4.21.-
UniProt
Q9Y337
Ligands
J08, NAG, NA
Pockets
1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 35% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BKallikrein-5 (EC 3.4.21.-)protein2279% helix, 35% strandQ9Y337

Ligands and binding sites

  • J08 · 4-[(5-phenyl-1~{H}-imidazol-2-yl)methylamino]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide · ligand · 2 copies · chains A, B
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
  • NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19750.780.8084J08

Interfaces

1 interface between chains.

  • A–B · 450 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

  • 6QFE · Crystal Structure of Human Kallikrein 5 in complex with GSK144 · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9Y337 · AlphaFold monomer V2.0 prediction for kallikrein-5 (Q9Y337) · a predicted model of the same protein · chain A against A, TM-score 0.99

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