Receptor
PDB id Resolution Class Description Source Keywords
3ACA 2.05 Å EC: 3.6.1.13 CRYSTAL STRUCTURE OF HUMAN NUDT5 COMPLEXED WITH 8-OXO-DADP A MANGANESE HOMO SAPIENS NUDIX MOTIF MAGNESIUM HYDROLASE-HYDROLASE INHIBITOR COMPLE
Ref.: DIVERSE SUBSTRATE RECOGNITION AND HYDROLYSIS MECHAN HUMAN NUDT5 NUCLEIC ACIDS RES. V. 39 8972 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8DD A:2;
B:209;
Valid;
Valid;
none;
none;
submit data
427.201 C10 H15 N5 O10 P2 c1nc(...
MN A:3;
A:4;
A:5;
B:1;
B:2;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ACA 2.05 Å EC: 3.6.1.13 CRYSTAL STRUCTURE OF HUMAN NUDT5 COMPLEXED WITH 8-OXO-DADP A MANGANESE HOMO SAPIENS NUDIX MOTIF MAGNESIUM HYDROLASE-HYDROLASE INHIBITOR COMPLE
Ref.: DIVERSE SUBSTRATE RECOGNITION AND HYDROLYSIS MECHAN HUMAN NUDT5 NUCLEIC ACIDS RES. V. 39 8972 2011
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3AC9 - 8GD C10 H15 N5 O11 P2 C1[C@@H]([....
2 3L85 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
3 3ACA - 8DD C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2DSC - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
5 3BM4 - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3AC9 - 8GD C10 H15 N5 O11 P2 C1[C@@H]([....
2 3L85 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
3 3ACA - 8DD C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2DSC - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
5 3BM4 - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3AC9 - 8GD C10 H15 N5 O11 P2 C1[C@@H]([....
2 3L85 - 8OG C10 H14 N5 O8 P C1[C@@H]([....
3 3ACA - 8DD C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2DSC - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
5 3BM4 - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 8DD; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 8DD 1 1
2 8OD 0.629214 0.934211
3 H6Y 0.574468 0.934211
4 8GD 0.520833 0.845238
5 8OP 0.505376 0.921053
6 8OX 0.5 0.805195
7 TYD 0.473118 0.8125
8 8DG 0.470588 0.845238
9 DUD 0.467391 0.844156
10 YYY 0.457447 0.835443
11 TTP 0.424242 0.8125
12 DAT 0.42 0.921053
13 DUT 0.418367 0.844156
14 6U4 0.415094 0.841463
15 DCP 0.41 0.835443
16 8OG 0.4 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ACA; Ligand: 8DD; Similar sites found: 14
This union binding pocket(no: 1) in the query (biounit: 3aca.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CBZ ATP 0.01784 0.41173 2.55102
2 2X1E X1E 0.01306 0.41186 3.06122
3 2J5V PCA 0.01298 0.42716 3.57143
4 3W9F I3P 0.01436 0.44783 4.08163
5 1JI0 ATP 0.02248 0.40629 4.59184
6 4L2I NAD 0.02267 0.40088 4.59184
7 4PPF FLC 0.02652 0.41164 5.61225
8 5BRP PNG 0.02369 0.40364 5.61225
9 4J7H TLO 0.001027 0.43216 6.63265
10 5GG9 8GT 0.0007542 0.41678 8.67347
11 3O61 GDD 0.00000008706 0.60479 27.2251
12 1VHZ APR 0.006684 0.43568 35.2041
13 5C8L GLC 0.0000007441 0.56572 39.5604
14 2YVO AMP 0.0008108 0.42942 41.7582
Pocket No.: 2; Query (leader) PDB : 3ACA; Ligand: 8DD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3aca.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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