4QPP

The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with compound DS-421 (2-{4-[3-CHLORO-2-(2-METHOXYPHENYL)-1H-INDOL-5-YL]PIPERIDIN-1-YL}-N-METHYLETHANAMINE

• PDB DOI: https://doi.org/10.2210/pdb4QPP/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-06-24 Released: 2014-08-20 
• Deposition Author(s): Dong, A., Zeng, H., Smil, D., Walker, J.R., He, H., Eram, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.234 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

The Crystal Structure of Human HMT1 hnRNP methyltransferase-like protein 6 in complex with compound DS-421

Zeng, H., Dong, A., Smil, D., Walker, J.R., He, H., Eram, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Brown, P.J., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130.41 kDa 
• Atom Count: 8,218 
• Modelled Residue Count: 1,001 
• Deposited Residue Count: 1,149 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A, B, C	376	Homo sapiens	Mutation(s): 1  Gene Names: HRMT1L6, PRMT6 EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens) Explore Q96LA8  Go to UniProtKB:  Q96LA8
PHAROS:  Q96LA8 GTEx:  ENSG00000198890

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POLY-UNK	D, E, F	7	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
36S	H [auth A], J [auth B], L [auth C]	2-{4-[3-chloro-2-(2-methoxyphenyl)-1H-indol-5-yl]piperidin-1-yl}-N-methylethanamine C23 H28 Cl N3 O SEJLXUYMIRXRMJ-UHFFFAOYSA-N
SAH	G [auth A], I [auth B], K [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.234 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.884	α = 90
b = 133.884	β = 90
c = 133.419	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Dong, A., Zeng, H., Smil, D., Walker, J.R., He, H., Eram, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-03-13
  Changes: Source and taxonomy