3I97

B1 domain of human Neuropilin-1 bound with small molecule EG00229

Structural Biology Knowledgebase: 3I97 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3I97

Classification: SIGNALING PROTEIN

Total Structure Weight: 36922.02

Macromolecule Entities
Molecule Chains Length Organism Details
Neuropilin-1 A, B 158 Homo sapiens Fragment: domain B1, F5/8 type C 1
Gene Name(s): NRP1 Gene View NRP VEGF165R

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
8DR
Query on 8DR

A, B (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene- 2-carboxamido)-5-guanidinopentanoic acid
1, (Synonym)
C17 H19 N7 O5 S3
ZWWMEDURALZMEV-NSHDSACASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
8DR IC50: 3000 - 23000 nM (100) BindingDB

N/A in BindingMoad
IC50: 3000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.216
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.00 α = 90.00
b = 89.60 β = 97.70
c = 41.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-10
  • Released Date: 2010-03-02
  • Deposition author(s): Allerston, C.K., Djordjevic, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4