1NF7

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


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of Human Inosine Monophosphate Dehydrogenase type II complexed with the MPA/NAD analog C2-MAD

Risal, D.Strickler, M.D.Goldstein, B.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase 2
A, B
514Homo sapiensMutation(s): 0 
Gene Names: IMPDH2
EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens)
Explore P12268 
Go to UniProtKB:  P12268
PHAROS:  P12268
GTEx:  ENSG00000178035 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12268
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYD
Query on MYD

Download Ideal Coordinates CCD File 
E [auth A],
H [auth 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
C23 H29 N5 O13 P2
AMYUZLUBFKOUEX-JKWAKEATSA-N
RVP
Query on RVP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
RIBAVIRIN MONOPHOSPHATE
C8 H13 N4 O8 P
SDWIOXKHTFOULX-AFCXAGJDSA-N
UNK
Query on UNK

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
M [auth B]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MYD BindingDB:  1NF7 Ki: 250 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.58α = 90
b = 146.58β = 90
c = 128.92γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description