6MHM

Crystal structure of human acid ceramidase in covalent complex with carmofur


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report



Literature

Molecular Mechanism of Inhibition of Acid Ceramidase by Carmofur.

Dementiev, A.Joachimiak, A.Nguyen, H.Gorelik, A.Illes, K.Shabani, S.Gelsomino, M.Ahn, E.E.Nagar, B.Doan, N.

(2019) J Med Chem 62: 987-992

  • DOI: 10.1021/acs.jmedchem.8b01723
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human acid ceramidase (AC) is a lysosomal cysteine amidase, which has received a great deal of interest in recent years as a potential target for the development of new therapeutics against melanoma and glioblastoma tumors. Despite the strong interes ...

    Human acid ceramidase (AC) is a lysosomal cysteine amidase, which has received a great deal of interest in recent years as a potential target for the development of new therapeutics against melanoma and glioblastoma tumors. Despite the strong interest in obtaining structural information, only the structures of the apo-AC enzyme in its zymogen and activated conformations are available. In this work, the crystal structure of AC in complex with the covalent carmofur inhibitor is presented. Carmofur is an antineoplastic drug containing an electrophilic carbonyl reactive group that targets the catalytic cysteine. This novel structural data explains the basis of the AC inhibition, provides insights into the enzymatic properties of the protein, and is a great aid toward the structure-based drug design of potent inhibitors for AC, providing the detailed mechanism, which has eluded the scientific community for more than 30 years, of carmofur's mysterious 5-fluorouracil-independent antitumor activity.


    Organizational Affiliation

    Department of Neurosurgery, Mitchell Cancer Institute , University of South Alabama , Mobile , Alabama 36617 United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acid ceramidase subunit alphaA, C131Homo sapiensMutation(s): 2 
Gene Names: ASAH1ASAHHSD-33HSD33
EC: 3.5.1.23 (PDB Primary Data), 3.5.1 (UniProt)
Find proteins for Q13510 (Homo sapiens)
Explore Q13510 
Go to UniProtKB:  Q13510
NIH Common Fund Data Resources
PHAROS  Q13510
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acid ceramidase subunit betaB, D253Homo sapiensMutation(s): 1 
Gene Names: ASAH1ASAHHSD-33HSD33
EC: 3.5.1.23 (PDB Primary Data), 3.5.1 (UniProt)
Find proteins for Q13510 (Homo sapiens)
Explore Q13510 
Go to UniProtKB:  Q13510
NIH Common Fund Data Resources
PHAROS  Q13510
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G
3 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H
2 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
JRY
Query on JRY

Download CCD File 
B, D
hexylcarbamic acid
C7 H15 N O2
YAQPZDICKJDHTR-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.718α = 90
b = 68.65β = 120.73
c = 98.386γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary