4FA3

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with (R)-1-(naphthalen-2-ylsulfonyl)piperidine-3-carboxylic acid (86)

Structural Biology Knowledgebase: 4FA3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FA3

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE inhibitor

Total Structure Weight: 39161.63

Macromolecule Entities
Molecule Chains Length Organism Details
Aldo-keto reductase family 1 member C3 A 331 Homo sapiens Gene Name(s): AKR1C3 Gene View DDH1 HSD17B5 KIAA0119 PGFS
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
0SL
Query on 0SL

A (3R)-1-(naphthalen-2-ylsulfonyl)piperidine- 3-carboxylic acid
C16 H17 N O4 S
KTQWWYGLWQVHDM-CQSZACIVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0SL IC50: 32 - 30000 nM (86 - 100) BindingDB

IC50: 32 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.208
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.13 α = 90.00
b = 63.47 β = 90.00
c = 96.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-21
  • Released Date: 2012-10-10
  • Deposition author(s): Turnbull, A.P., Jamieson, S.M.F., Brooke, D.G., Heinrich, D., Atwell, G.J., Silva, S., Hamilton, E.J., Rigoreau, L.J.M., Trivier, E., Soudy, C., Samlal, S.S., Owen, P.J., Schroeder, E., Raynham, T., Flanagan, J.U., Denny, W.A.

Revision History

No revisions since initial release