3VZD

Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP

Structural Biology Knowledgebase: 3VZD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VZD

Classification: TRANSFERASE / INHIBITOR

Total Structure Weight: 242835.90

Macromolecule Entities
Molecule Chains Length Organism Details
Sphingosine kinase 1 A, B, C..., D, E, FA, B, C, D, E, F 361 Homo sapiens EC#: 2.7.1.91 IUBMB
Fragment: UNP RESIDUES 9-364
Gene Name(s): SPHK1 Gene View SPHK SPK

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

C, E ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UUL
Query on UUL

A, B, C, D, E, F 4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol
C15 H11 Cl N2 O S
ZFGXZJKLOFCECI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

B PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B, C, E CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, C, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UUL N/A in BindingDB
N/A in BindingMoad
IC50: 500 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.206
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.20 α = 90.00
b = 106.57 β = 90.00
c = 226.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-11
  • Released Date: 2013-05-01
  • Deposition author(s): Min, X., Walker, N.P., Wang, Z.

Revision History

  • 2014-01-29
    Type: Citation | Details: Citation update