6MHM | pdb_00006mhm

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 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

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: https://doi.org/10.1021/acs.jmedchem.8b01723
  • Primary Citation Related Structures: 
    6MHM

  • 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 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
    • Structural Biology Center, Biosciences Division , Argonne National Laboratory , Lemont , Illinois 60439 , United States.

Macromolecule Content 

  • Total Structure Weight: 92.45 kDa 
  • Atom Count: 6,208 
  • Modeled Residue Count: 734 
  • Deposited Residue Count: 768 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acid ceramidase subunit alpha
A, C
131Homo sapiensMutation(s): 2 
Gene Names: ASAH1ASAHHSD-33HSD33
EC: 3.5.1.23 (PDB Primary Data), 3.5.1 (UniProt), 3.5.1.109 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13510 (Homo sapiens)
Explore Q13510 
Go to UniProtKB:  Q13510
PHAROS:  Q13510
GTEx:  ENSG00000104763 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13510
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acid ceramidase subunit beta
B, D
253Homo sapiensMutation(s): 1 
Gene Names: ASAH1ASAHHSD-33HSD33
EC: 3.5.1.23 (PDB Primary Data), 3.5.1 (UniProt), 3.5.1.109 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13510 (Homo sapiens)
Explore Q13510 
Go to UniProtKB:  Q13510
PHAROS:  Q13510
GTEx:  ENSG00000104763 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13510
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q13510-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
L [auth B],
T [auth D],
U [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
JRY

Query on JRY



Download:Ideal Coordinates CCD File
M [auth B],
V [auth D]
hexylcarbamic acid
C7 H15 N O2
YAQPZDICKJDHTR-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
N [auth B]
O [auth B]
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary