8H4R

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

PDB DOI: https://doi.org/10.2210/pdb8H4R/pdb

Classification: CELL CYCLE
Organism(s): Schistosoma japonicum, Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-10-11 Released: 2023-10-11
Deposition Author(s): Gui, W., Wang, F., Cheng, W., Gao, J., Huang, Y., Ouyang, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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.

Macromolecule Content

Total Structure Weight: 98.85 kDa
Atom Count: 4,942
Modelled Residue Count: 562
Deposited Residue Count: 838
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3	A	533	Schistosoma japonicum, Homo 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P08515Q00526
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G1/S-specific cyclin-E1	B	305	Homo sapiens	Mutation(s): 0 Gene Names: CCNE1, CCNE
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24864
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1QK (Subject of Investigation/LOI) Query on 1QK Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	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		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B]	E [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]