Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T25462 Target Info
Target Name Mixed-lineage leukemia protein (MLL)
Synonyms p320; p180; Zinc finger protein HRX; Trithoraxlike protein; Trithorax-like protein; Myeloid/lymphoid or mixed-lineage leukemia protein 1; Myeloid/lymphoid or mixed-lineage leukemia; MLL1; MLL cleavage product C180; Lysine Nmethyltransferase 2A; Lysine N-methyltransferase 2A; Histonelysine Nmethyltransferase MLL; Histone-lysine N-methyltransferase 2A; HTRX; HRX; CXXCtype zinc finger protein 7; CXXC7; CXXC-type zinc finger protein 7; ALL1; ALL-1
Target Type Literature-reported Target
Gene Name KMT2A
Biochemical Class Methyltransferase
UniProt ID
KMT2A_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Glyoxalate, Glyoxylate Ligand Info
Structure Description Crystal structure of human menin in complex with MLL1 and LEDGF PDB:3U88
Method X-ray diffraction Resolution 3.00 Å Mutation No [1]
PDB Sequence
RWRFPARPGT
15
GRRGLGGAPR
32
QRVPALLRVG
109
PGFDAALQVS
119
AAIGTNLRRF
129

RAVFGE
Residue
Distance (Å)
TRP7
3.972
Residue
Distance (Å)
Ligand Name: 5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(4-chlorophenyl)methyl]azetidin-3-yl}methyl)amino}-5'-deoxyadenosine Ligand Info
Structure Description MLL1 SET N3861I/Q3867L bound to inhibitor 14 (TC-5139) PDB:6U9N
Method X-ray diffraction Resolution 1.95 Å Mutation Yes [2]
PDB Sequence
LPMPMRFRHL
3823
KKTSKEAVGV
3833
YRSPIHGRGL
3843
FCKRNIDAGE
3853
MVIEYAGIVI
3863

RSILTDKREK
3873
YYDSKGIGCY
3883
MFRIDDSEVV
3893
DATMHGNAAR
3903
FINHSCEPNC
3913

YSRVINIDGQ
3923
KHIVIFAMRK
3933
IYRGEELTYD
3943
YKKLPCNCGA
3961
KKCRKFL
Residue
Distance (Å)
ILE3838
3.325
HIS3839
2.333
GLY3840
3.256
ARG3841
2.828
GLY3842
4.782
GLY3881
3.472
CYS3882
2.459
TYR3883
2.559
ARG3903
3.074
PHE3904
2.515
Residue
Distance (Å)
ILE3905
3.296
ASN3906
1.956
HIS3907
1.843
SER3908
3.685
TYR3944
2.452
PRO3956
2.847
CYS3957
2.684
ASN3958
2.836
CYS3959
2.911
Ligand Name: 5'-([(3S)-3-amino-3-carboxypropyl]{[1-(3,3-diphenylpropyl)azetidin-3-yl]methyl}amino)-5'-deoxyadenosine Ligand Info
Structure Description MLL1 SET N3861I/Q3867L bound to inhibitor 18 (TC-5153) PDB:6U9K
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [2]
PDB Sequence
DLPMPMRFRH
3822
LKKTSKEAVG
3832
VYRSPIHGRG
3842
LFCKRNIDAG
3852
EMVIEYAGIV
3862

IRSILTDKRE
3872
KYYDSKGIGC
3882
YMFRIDDSEV
3892
VDATMHGNAA
3902
RFINHSCEPN
3912

CYSRVINIDG
3922
QKHIVIFAMR
3932
KIYRGEELTY
3942
DYKFKLPCNC
3959
GAKKCRKFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q2V or .Q2V2 or .Q2V3 or :3Q2V;style chemicals stick;color identity;select .A:3838 or .A:3839 or .A:3840 or .A:3841 or .A:3842 or .A:3879 or .A:3880 or .A:3881 or .A:3882 or .A:3883 or .A:3903 or .A:3904 or .A:3905 or .A:3906 or .A:3907 or .A:3908 or .A:3944 or .A:3946 or .A:3955 or .A:3956 or .A:3957 or .A:3958 or .A:3959 or .A:3968; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE3838
3.279
HIS3839
2.669
GLY3840
3.775
ARG3841
1.752
GLY3842
3.977
GLY3879
2.564
ILE3880
3.762
GLY3881
3.149
CYS3882
1.911
TYR3883
2.674
ARG3903
3.203
PHE3904
2.610
Residue
Distance (Å)
ILE3905
3.295
ASN3906
2.026
HIS3907
1.813
SER3908
3.742
TYR3944
2.401
PHE3946
4.149
LEU3955
4.681
PRO3956
2.720
CYS3957
2.573
ASN3958
2.869
CYS3959
2.934
LEU3968
3.081
Ligand Name: 5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(thiophen-2-yl)methyl]azetidin-3-yl}methyl)amino}-5'-deoxyadenosine Ligand Info
Structure Description MLL1 SET N3861I/Q3867L bound to inhibitor 16 (TC-5109) PDB:6U9M
Method X-ray diffraction Resolution 2.05 Å Mutation Yes [2]
PDB Sequence
LPMPMRFRHL
3823
KKTSKEAVGV
3833
YRSPIHGRGL
3843
FCKRNIDAGE
3853
MVIEYAGIVI
3863

RSILTDKREK
3873
YYDSKGIGCY
3883
MFRIDDSEVV
3893
DATMHGNAAR
3903
FINHSCEPNC
3913

YSRVINIDGQ
3923
KHIVIFAMRK
3933
IYRGEELTYD
3943
YKFKLPCNCG
3960
AKKCRKFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q2M or .Q2M2 or .Q2M3 or :3Q2M;style chemicals stick;color identity;select .A:3838 or .A:3839 or .A:3840 or .A:3841 or .A:3842 or .A:3881 or .A:3882 or .A:3883 or .A:3903 or .A:3904 or .A:3905 or .A:3906 or .A:3907 or .A:3908 or .A:3944 or .A:3956 or .A:3957 or .A:3958 or .A:3959 or .A:3968; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE3838
3.289
HIS3839
2.402
GLY3840
3.389
ARG3841
2.742
GLY3842
4.847
GLY3881
3.389
CYS3882
2.174
TYR3883
2.604
ARG3903
3.026
PHE3904
2.461
Residue
Distance (Å)
ILE3905
3.339
ASN3906
1.927
HIS3907
1.960
SER3908
3.848
TYR3944
2.466
PRO3956
2.680
CYS3957
2.651
ASN3958
2.855
CYS3959
2.957
LEU3968
2.984
Ligand Name: 5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(3-chlorophenyl)methyl]azetidin-3-yl}methyl)amino}-5'-deoxyadenosine Ligand Info
Structure Description MLL1 SET N3861I/Q3867L bound to inhibitor 12 (TC-5140) PDB:6U9R
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [2]
PDB Sequence
DLPMPMRFRH
3822
LKKTSKEAVG
3832
VYRSPIHGRG
3842
LFCKRNIDAG
3852
EMVIEYAGIV
3862

IRSILTDKRE
3872
KYYDSKGIGC
3882
YMFRIDDSEV
3892
VDATMHGNAA
3902
RFINHSCEPN
3912

CYSRVINIDG
3922
QKHIVIFAMR
3932
KIYRGEELTY
3942
DYKFKLPCNC
3959
GAKKCRKFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Q2P or .Q2P2 or .Q2P3 or :3Q2P;style chemicals stick;color identity;select .A:3838 or .A:3839 or .A:3840 or .A:3841 or .A:3842 or .A:3881 or .A:3882 or .A:3883 or .A:3903 or .A:3904 or .A:3905 or .A:3906 or .A:3907 or .A:3908 or .A:3944 or .A:3946 or .A:3956 or .A:3957 or .A:3958 or .A:3959; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE3838
3.405
HIS3839
2.026
GLY3840
3.525
ARG3841
1.902
GLY3842
4.049
GLY3881
3.230
CYS3882
2.068
TYR3883
2.557
ARG3903
3.026
PHE3904
2.521
Residue
Distance (Å)
ILE3905
3.321
ASN3906
2.631
HIS3907
1.939
SER3908
3.713
TYR3944
2.318
PHE3946
4.513
PRO3956
2.909
CYS3957
2.761
ASN3958
2.866
CYS3959
2.909
References  Top
REF 1 The same pocket in menin binds both MLL and JUND but has opposite effects on transcription. Nature. 2012 Feb 12;482(7386):542-6.
REF 2 Discovery of Potent Small-Molecule Inhibitors of MLL Methyltransferase. ACS Med Chem Lett. 2020 May 14;11(6):1348-1352.

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