1NF7

Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with Ribavirin Monophosphate and C2-Mycophenolic Adenine Dinucleotide

Structural Biology Knowledgebase: 1NF7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.238

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NF7

Classification: OXIDOREDUCTASE

Total Structure Weight: 114902.61

Macromolecule Entities
Molecule Chains Length Organism Details
Inosine-5'-monophosphate dehydrogenase 2 A, B 514 Homo sapiens EC#: 1.1.1.205 IUBMB
Gene Name(s): IMPDH2 Gene View IMPD2

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

A, B {[5-(6-AMINO-PURIN-7-YL)-3,4-DIHYDROXY-TETRAHYDRO- FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}- PHOSPHONIC ACID MONO-[2-(4-HYDROXY-6-METHOXY- 7-METHYL-3-OXO-1,3-DIHYDRO-ISOBENZOFURAN- 5-YL)-ETHYL] ESTER
C2-MYCOPHENOLIC ADENINE DINUCLEOTIDE (Synonym)
C23 H29 N5 O13 P2
AMYUZLUBFKOUEX-JKWAKEATSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RVP
Query on RVP

A, B RIBAVIRIN MONOPHOSPHATE
C8 H13 N4 O8 P
SDWIOXKHTFOULX-AFCXAGJDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNK
Query on UNK

B UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MYD Ki: 250 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.238
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.58 α = 90.00
b = 146.58 β = 90.00
c = 128.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-13
  • Released Date: 2004-01-27
  • Deposition author(s): Risal, D., Strickler, M.D., Goldstein, B.M.

Revision History

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