4Q6R

Crystal structure of human sphingosine-1-phosphate lyase in complex with inhibitor 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 4Q6R

Classification: Lyase / Lyase inhibitor

Total Structure Weight: 114950.23

Macromolecule Entities
Molecule Chains Length Organism Details
Sphingosine-1-phosphate lyase 1 A, B 511 Homo sapiens EC#: 4.1.2.27 IUBMB
Gene Name(s): SGPL1 Gene View KIAA1252
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
30J
Query on 30J

A, B 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1- yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile
C26 H23 Cl N6
XUZUIICAPXZZDU-GOSISDBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SIN
Query on SIN

A SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
30J IC50: 210 nM (100) BindingDB

IC50: 210 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
LLP
Query on LLP
A, B L-PEPTIDE LINKING C14 H22 N3 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.178
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 127.99 α = 90.00
b = 130.53 β = 90.00
c = 68.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-04-23
  • Released Date: 2014-05-21
  • Deposition author(s): Srinivas, H.

Revision History

  • Version 1_0: 2014-05-21

    Type: Initial release

  • Version 1_1: 2014-07-23

    Type: Database references