10AX | pdb_000010ax

Crystal structure of human SMYD1 in complex with Sinefungin

• PDB DOI: https://doi.org/10.2210/pdb10AX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2026-01-09 Released: 2026-09-02 
• Deposition Author(s): Zeng, H., Dong, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.288 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human SMYD1 in complex with Sinefungin

Zeng, H., Dong, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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: 56.26 kDa 
• Atom Count: 3,572 
• Modeled Residue Count: 448 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SMYD1	A	482	Homo sapiens	Mutation(s): 0  Gene Names: SMYD1 EC: 2.1.1.354
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB12 (Homo sapiens) Explore Q8NB12  Go to UniProtKB:  Q8NB12
PHAROS:  Q8NB12 GTEx:  ENSG00000115593

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG (Subject of Investigation/LOI)	E [auth A]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	F [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.288 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.108	α = 90
b = 105.108	β = 90
c = 206.621	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Zeng, H., Dong, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release