5XXG | pdb_00005xxg

Crystal structure of SmyD3 in complex with covalent inhibitor 2

• PDB DOI: https://doi.org/10.2210/pdb5XXG/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-03 Released: 2018-08-08 
• Deposition Author(s): Baburajendran, N., Jansson, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure of SmyD3 in complex with covalent inhibitor 2

Baburajendran, N., Jansson, E.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.64 kDa 
• Atom Count: 3,574 
• Modeled Residue Count: 423 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SMYD3	A	423	Homo sapiens	Mutation(s): 0  EC: 2.1.1.354
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens) Explore Q9H7B4  Go to UniProtKB:  Q9H7B4
PHAROS:  Q9H7B4 GTEx:  ENSG00000185420

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8HR	B [auth A]	propyl 4-(4-chloranyl-2-phenyl-quinolin-7-yl)carbonylpiperazine-1-carboxylate C24 H24 Cl N3 O3 KSURKAFQFJOCBC-UHFFFAOYSA-N
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8HR	BindingDB:  5XXG	Ki: 3900 (nM) from 1 assay(s)
		IC50: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.288	α = 90
b = 66.374	β = 90
c = 107.296	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Baburajendran, N., Jansson, E.A.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary