Receptor
PDB id Resolution Class Description Source Keywords
6N0Y 2.2 Å EC: 4.1.1.33 CRYSTAL STRUCTURE OF ANAEROLINEA THERMOPHILA MEVALONATE 5-PH DECARBOXYLASE COMPLEXED WITH (R)-MVAPP ANAEROLINEA THERMOPHILA (STRAIN DSM 1411388 / NBRC 100420 / UNI-1) LYASE
Ref.: SUBSTRATE SPECIFICITY AND ENGINEERING OF MEVALONATE 5-PHOSPHATE DECARBOXYLASE. ACS CHEM.BIOL. V. 14 1767 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DP6 F:401;
A:401;
E:401;
B:401;
D:401;
C:401;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 Atoms found MORE than expected: % Diff = 2;
none;
none;
none;
none;
Atoms found MORE than expected: % Diff = 2;
 submit data
308.117 C6 H14 O10 P2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6N0X 1.44 Å EC: 4.1.1.33 CRYSTAL STRUCTURE OF ANAEROLINEA THERMOPHILA MEVALONATE 5-PH DECARBOXYLASE COMPLEXED WITH (R)-MVAP ANAEROLINEA THERMOPHILA (STRAIN DSM 1411388 / NBRC 100420 / UNI-1) LYASE
Ref.: SUBSTRATE SPECIFICITY AND ENGINEERING OF MEVALONATE 5-PHOSPHATE DECARBOXYLASE. ACS CHEM.BIOL. V. 14 1767 2019
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6N0Z - DP6 C6 H14 O10 P2 C[C@@](CCO....
2 6N0X - PMV C6 H13 O7 P C[C@@](CCO....
3 6N0Y - DP6 C6 H14 O10 P2 C[C@@](CCO....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6N0Z - DP6 C6 H14 O10 P2 C[C@@](CCO....
2 6N0X - PMV C6 H13 O7 P C[C@@](CCO....
3 6N0Y - DP6 C6 H14 O10 P2 C[C@@](CCO....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4DU8 - 2P0 C7 H13 N O10 P2 C1C[C@H](N....
2 4DPY - 2P0 C7 H13 N O10 P2 C1C[C@H](N....
3 4DPT - FM0 C6 H13 F O10 P2 C(CO[P@](=....
4 3QT6 Ki = 4.3 uM 2P0 C7 H13 N O10 P2 C1C[C@H](N....
5 4DPU - FM0 C6 H13 F O10 P2 C(CO[P@](=....
6 3QT7 Ki = 49 uM FM0 C6 H13 F O10 P2 C(CO[P@](=....
7 4DU7 - DP6 C6 H14 O10 P2 C[C@@](CCO....
8 3QT8 - FM0 C6 H13 F O10 P2 C(CO[P@](=....
9 5GME - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
10 5GMD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
11 6N0Z - DP6 C6 H14 O10 P2 C[C@@](CCO....
12 6N0X - PMV C6 H13 O7 P C[C@@](CCO....
13 6N0Y - DP6 C6 H14 O10 P2 C[C@@](CCO....
14 6E2V - DP6 C6 H14 O10 P2 C[C@@](CCO....
15 6E2W - DP6 C6 H14 O10 P2 C[C@@](CCO....
16 6E2U - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
17 6E2Y - DP6 C6 H14 O10 P2 C[C@@](CCO....
18 5V2L - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 6E2T - DP6 C6 H14 O10 P2 C[C@@](CCO....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DP6; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 DP6 1 1
2 PMV 0.731707 1
3 BHI 0.644444 0.878049
4 FM0 0.58 0.853659
5 P23 0.422222 0.794872
6 1CO 0.422222 0.625
7 IPR 0.416667 0.8
8 0CJ 0.411765 0.85
9 IPE 0.408163 0.785714
Similar Ligands (3D)
Ligand no: 1; Ligand: DP6; Similar ligands found: 3
No: Ligand Similarity coefficient
1 2P0 0.8803
2 BTN 0.8609
3 6KJ 0.8566
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6N0X; Ligand: PMV; 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: 6n0x.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6N0X; Ligand: PMV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6n0x.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6N0X; Ligand: PMV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6n0x.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6N0X; Ligand: PMV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6n0x.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6N0X; Ligand: PMV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6n0x.bio3) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6N0X; Ligand: PMV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 6n0x.bio3) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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