Receptor
PDB id Resolution Class Description Source Keywords
2AZM 2.41 Å NON-ENZYME: CELL_CYCLE CRYSTAL STRUCTURE OF THE MDC1 BRCT REPEAT IN COMPLEX WITH THE HISTONE TAIL OF GAMMA-H2AX HOMO SAPIENS BRCT REPEAT PROTEIN-PHOSPHOPEPTIDE COMPLEX DNA DAMAGE CELL CYCLE
Ref.: MDC1 DIRECTLY BINDS PHOSPHORYLATED HISTONE H2AX TO REGULATE CELLULAR RESPONSES TO DNA DOUBLE-STRAND BREAKS CELL(CAMBRIDGE,MASS.) V. 123 1213 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LYS LYS ALA THR GLN ALA SEP GLN GLU TYR C:138;
D:138;
 Valid;
Valid;
 none;
none;
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672.541 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3K05 1.33 Å NON-ENZYME: CELL_CYCLE THE CRYSTAL STRUCTURE OF MDC1 BRCT T2067D IN COMPLEX WITH A RECOGNITION TETRAPEPTIDE WITH AN AMIDATED C-TERMINUS HOMO SAPIENS BRCT DOMAIN PROTEIN-PEPTIDE COMPLEX PHOSPHO PROTEIN BINDINDNA DAMAGE RESPONSE CELL CYCLE DNA DAMAGE DNA REPAIR NUPHOSPHOPROTEIN PROTEIN BINDING
Ref.: COMPARISON OF THE STRUCTURES AND PEPTIDE BINDING SPECIFICITIES OF THE BRCT DOMAINS OF MDC1 AND BRCA1 STRUCTURE V. 18 167 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 2AZM - LYS LYS ALA THR GLN ALA SEP GLN GLU TYR n/a n/a
2 3K05 Ki = 51 uM SEP GLN GLU TYR NH2 n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 2AZM - LYS LYS ALA THR GLN ALA SEP GLN GLU TYR n/a n/a
2 3K05 Ki = 51 uM SEP GLN GLU TYR NH2 n/a n/a
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 2AZM - LYS LYS ALA THR GLN ALA SEP GLN GLU TYR n/a n/a
2 3K05 Ki = 51 uM SEP GLN GLU TYR NH2 n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LYS LYS ALA THR GLN ALA SEP GLN GLU TYR; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS LYS ALA THR GLN ALA SEP GLN GLU TYR 1 1
2 SEP GLN GLU TYR NH2 0.591398 0.981481
3 GLU GLU GLN GLU GLU TYR 0.571429 0.740741
4 SEP GLN GLU PTR 0.5625 0.962963
5 THR ASN GLU PHE TYR PHE 0.520833 0.689655
6 GLU ASN GLN LYS GLU TYR PHE PHE 0.504673 0.677419
7 TYR GLN PHE 0.5 0.696429
8 SER GLN ASN TYR 0.5 0.77193
9 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.490385 0.677966
10 PRO GLU SEP LEU GLU SER CYS PHE 0.482143 0.816667
11 VAL TYR 0.47561 0.625
12 THR ASN GLU TYR TYR VAL 0.469388 0.683333
13 ALA THR LYS ALA SEP GLN GLU LEU 0.464646 0.789474
14 GLY GLU GLU GLU GLY GLU CYS TYR 0.456311 0.694915
15 SER SER ARG LYS GLU TYR TYR ALA 0.455357 0.651515
16 ALA ARG THR MLY GLN THR ALA ARG TYR 0.447154 0.643836
17 SER ASP TYR GLN ARG LEU 0.445455 0.6875
18 GLU LEU LYS TPO GLU ARG TYR 0.44186 0.80303
19 LYS PRO SEP GLN GLU LEU 0.4375 0.671429
20 ASP SEP TYR GLU VAL LEU ASP LEU 0.4375 0.929825
21 ALA THR ALA ALA ALA THR GLU ALA TYR 0.433962 0.767857
22 TYR GLU TRP 0.433962 0.629032
23 TYR PHE SER SEP ASN 0.432432 0.847458
24 VAL TYR ARG SER LEU SEP PHE GLU 0.431034 0.813559
25 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.428571 0.716667
26 THR ASN GLU TYR LYS VAL 0.427273 0.704918
27 THR ASN GLU PHE TYR ALA 0.423423 0.728814
28 ACE ILE TYR GLU SER LEU 0.422018 0.716667
29 TYR ALA GLY SEP TPO ASP GLU ASN 0.413534 0.868852
30 THR LYS ASN TYR LYS GLN PHE SER VAL 0.413223 0.730159
31 GLY GLY LYS LYS LYS TYR GLN LEU 0.408696 0.677419
32 ASP ALA ASP GLU TYR LEU 0.405405 0.736842
33 ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.404959 0.698413
34 ALA GLU THR PHE 0.40404 0.696429
35 THR ASN GLU PHE ALA PHE 0.403846 0.62069
36 SER GLN TYR TYR TYR ASN SER LEU 0.401786 0.725806
37 LYS ARG ARG ARG LYS SEP CYS GLN ALA NH2 0.401709 0.681818
38 CYS THR GLU LEU LYS LEU ASN ASP TYR 0.401575 0.714286
39 GLY ALA PHE THR PHE ASN GLU ASP PHE 0.4 0.706897
40 TYR GLN SER LYS LEU 0.4 0.737705
41 TYR ASP GLN ILE LEU 0.4 0.706897
Similar Ligands (3D)
Ligand no: 1; Ligand: LYS LYS ALA THR GLN ALA SEP GLN GLU TYR; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3K05; Ligand: SEP GLN GLU TYR NH2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3k05.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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