8QDI

compound 1b bound KMT9 crystal structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 

Starting Model: experimental
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Literature

compound 1a bound KMT9 crystal structure

Sheng, W., Eric, M., Roland, S.

To be published.

Macromolecules
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(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
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  • Reference Sequence
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(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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QII (Subject of Investigation/LOI)
Query on QII
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-[2-[(2~{R})-pyrrolidin-2-yl]ethyl]amino]-2-azanyl-butanoic acid
C20 H32 N8 O5
HVEHZOYFHBQABO-DAEWCUBLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.516α = 90
b = 110.516β = 90
c = 129.837γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1381
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: 2024-09-11
    Type: Initial release