Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T90766 Target Info
Target Name Mutated Histone H3.3 (H3F3A)
Synonyms PP781; Histone H3.3; H3F3; H3.3B; H3.3A
Target Type Literature-reported Target
Gene Name H3F3A
UniProt ID
H33_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Tilarginine Ligand Info
Structure Description Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) PDB:5DWQ
Method X-ray diffraction Resolution 2.36 Å Mutation Yes [1]
PDB Sequence
GKAPKQLA
Residue
Distance (Å)
ALA3
3.215
PRO4
1.331
Residue
Distance (Å)
LYS6
1.328
GLN7
4.036
Ligand Name: Flavin-Adenine Dinucleotide Ligand Info
Structure Description Crystal structure of LSD2-NPAC with H3 in space group P3221 PDB:4GUS
Method X-ray diffraction Resolution 2.23 Å Mutation Yes [2]
PDB Sequence
ARTMQTARKS
10
TGGKAPRKQL
20
Residue
Distance (Å)
MET4
4.505
Residue
Distance (Å)
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Ligand Name: Sinefungin Ligand Info
Structure Description Crystal structure of CARM1, sinefungin, and H3 peptide (R17) PDB:5DX0
Method X-ray diffraction Resolution 2.05 Å Mutation Yes [1]
PDB Sequence
GKAPRKQL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SFG or .SFG2 or .SFG3 or :3SFG;style chemicals stick;color identity;select .F:5; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG5
3.061
Residue
Distance (Å)
Ligand Name: Tetrachloroplatinate(II) Ligand Info
Structure Description Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX PDB:4HGA
Method X-ray diffraction Resolution 2.80 Å Mutation No [3]
PDB Sequence
PGTVALREIR
52
RYQKSTELLI
62
RKLPFQRLVR
72
EIAQDFKTDL
82
RFQSAAIGAL
92

QEASEAYLVG
102
LFEDTNLCAI
112
HAKRVTIMPK
122
DIQLARRIRG
132
ERA
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PC4 or .PC42 or .PC43 or :3PC4;style chemicals stick;color identity;select .B:120 or .B:121; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET120
3.115
Residue
Distance (Å)
PRO121
4.888
Ligand Name: (2~{r},3~{r},4~{s},5~{r})-2-(6-Aminopurin-9-Yl)-5-[(~{e})-Prop-1-Enyl]oxolane-3,4-Diol Ligand Info
Structure Description Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated PDB:7OKP
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [4]
PDB Sequence
GKAPRQLAT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QVR or .QVR2 or .QVR3 or :3QVR;style chemicals stick;color identity;select .E:16 or .E:17; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PRO16
4.972
Residue
Distance (Å)
ARG17
1.457
Ligand Name: N6-Acetyl-L-lysine Ligand Info
Structure Description Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated PDB:7OKP
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [4]
PDB Sequence
GKAPRQLAT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ALY or .ALY2 or .ALY3 or :3ALY;style chemicals stick;color identity;select .E:13 or .E:14 or .E:15 or .E:16 or .E:17 or .E:19 or .E:20; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY13
4.496
LYS14
3.280
ALA15
2.261
PRO16
4.002
Residue
Distance (Å)
ARG17
1.327
GLN19
1.323
LEU20
3.350
References  Top
REF 1 Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates. ACS Chem Biol. 2016 Mar 18;11(3):763-71.
REF 2 LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell. 2013 Feb 7;49(3):558-70.
REF 3 Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX. Nat Struct Mol Biol. 2012 Dec;19(12):1287-92.
REF 4 Structural Studies Provide New Insights into the Role of Lysine Acetylation on Substrate Recognition by CARM1 and Inform the Design of Potent Peptidomimetic Inhibitors. Chembiochem. 2021 Dec 10;22(24):3469-3476.

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