8H4R

The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.161 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus

Gui, W.Wang, F.Cheng, W.Gao, J.Huang, Y.Ouyang, Z.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3533Schistosoma japonicumHomo sapiens
This entity is chimeric
Mutation(s): 0 
EC: 2.5.1.18 (PDB Primary Data), 2.7.11.22 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P08515 (Schistosoma japonicum)
Explore P08515 
Go to UniProtKB:  P08515
Find proteins for Q00526 (Homo sapiens)
Explore Q00526 
Go to UniProtKB:  Q00526
PHAROS:  Q00526
GTEx:  ENSG00000250506 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP08515Q00526
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G1/S-specific cyclin-E1305Homo sapiensMutation(s): 0 
Gene Names: CCNE1CCNE
UniProt & NIH Common Fund Data Resources
Find proteins for P24864 (Homo sapiens)
Explore P24864 
Go to UniProtKB:  P24864
PHAROS:  P24864
GTEx:  ENSG00000105173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24864
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1QK (Subject of Investigation/LOI)
Query on 1QK

Download Ideal Coordinates CCD File 
C [auth A]3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium
C21 H29 N6 O2
WBUFFOKXERTKGU-SFHVURJKSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
K [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
F [auth B]
G [auth B]
H [auth B]
I [auth B]
D [auth A],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.161 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.027α = 90
b = 155.027β = 90
c = 76.788γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary