5XXJ | pdb_00005xxj

Crystal structure of SmyD3 in complex with covalent inhibitor 3

• PDB DOI: https://doi.org/10.2210/pdb5XXJ/pdb

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


• Deposited: 2017-07-04 Released: 2018-08-08 
• Deposition Author(s): Baburajendran, N., Jansson, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of SmyD3 in complex with covalent inhibitor 3

Baburajendran, N., Jansson, A.E.

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: 49.71 kDa 
• Atom Count: 3,569 
• 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
8HF (Subject of Investigation/LOI)	E [auth A]	propyl (2~{R})-4-[4-chloranyl-2-[4-(2-oxidanylpropan-2-yl)phenyl]quinolin-7-yl]carbonyl-2-methyl-piperazine-1-carboxylate C28 H32 Cl N3 O4 BURBRCSDCXUEJO-GOSISDBHSA-N
SAM	F [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.386	α = 90
b = 66.45	β = 90
c = 108.042	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary