6H0W

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS035


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 

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This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS035

Malecki, P.H.Weiss, M.S.Heinemann, U.Link, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 4DA342Homo sapiensMutation(s): 0 
Gene Names: KDM4DJHDM3DJMJD2D
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens)
Explore Q6B0I6 
Go to UniProtKB:  Q6B0I6
PHAROS:  Q6B0I6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
Q [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
FHW (Subject of Investigation/LOI)
Query on FHW

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P [auth A](2~{R})-3-phenyl-2-(2~{H}-1,2,3,4-tetrazol-5-yl)propanehydrazide
C10 H12 N6 O
SGFUQCKYWZCXFN-MRVPVSSYSA-N
 Ligand Interaction
I1L
Query on I1L

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R [auth A][2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoylamino]azanium
C3 H7 N6 O
TWKUAKLZOIABHJ-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

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M [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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N [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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O [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.482α = 90
b = 71.482β = 90
c = 150.707γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release