9FL4 | pdb_00009fl4

compound 5b bound KMT9 crystal structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.182 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.152 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

compound 5b bound KMT9 crystal structure

Sheng, W., Eric, M., Roland, S.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase N6AMT1203Homo sapiensMutation(s): 0 
Gene Names: N6AMT1, C21orf127, HEMK2, KMT9, PRED28
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5N5 (Homo sapiens)
Explore Q9Y5N5 
Go to UniProtKB:  Q9Y5N5
PHAROS:  Q9Y5N5
GTEx:  ENSG00000156239 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5N5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like protein126Homo sapiensMutation(s): 0 
Gene Names: TRMT112, AD-001, HSPC152, HSPC170
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI30 (Homo sapiens)
Explore Q9UI30 
Go to UniProtKB:  Q9UI30
PHAROS:  Q9UI30
GTEx:  ENSG00000173113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IC6 (Subject of Investigation/LOI)
Query on A1IC6
Download Ideal Coordinates CCD File 
C [auth A](2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-(2-phenylethylamino)propyl]amino]-2-azanyl-butanoic acid
C25 H36 N8 O5
RUEKXDREIULVAB-XCPBYIKRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.182 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.152 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.538α = 90
b = 110.538β = 90
c = 131.119γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB992
German Research Foundation (DFG)GermanySchu688
German Research Foundation (DFG)GermanyEXC-2189
German Research Foundation (DFG)GermanyDKTK FR01-374

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release