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MolNFT v1 · #27794 · protein

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor

1XUC · Collagenase 3: “Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor”. X-ray diffraction, 3 ligands (PB3, ZN, CA), 1 pocket (best druggability 0.76). MolNFT v1 #27794 on GenesisL1: 3D structure, binding sites and…

PDB
1XUC
Type
protein
Length
335 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Collagenase 3
EC
3.4.24.-
UniProt
P45452
Ligands
PB3, ZN, CA
Pockets
1 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACollagenase 3 (EC 3.4.24.-)protein16924% helix, 18% strandP45452
BCollagenase 3 (EC 3.4.24.-)protein16623% helix, 18% strandP45452

Ligands and binding sites

  • PB3 · N,N'-bis(3-methylbenzyl)pyrimidine-4,6-dicarboxamide · ligand · 2 copies · chains A, B
  • ZN · Zinc ion · metal · 4 copies · chains A, B
  • CA · Calcium ion · metal · 4 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
19160.760.79121PB3

Interfaces

1 interface between chains.

  • A–B · 1222 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

  • 1XUC · Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
  • P45452 · AlphaFold monomer V2.0 prediction for collagenase 3 (P45452) · a predicted model of the same protein · chain B against A, TM-score 0.95

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