Receptor
PDB id Resolution Class Description Source Keywords
3HWW 1.95 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF MENAQUINONE SYNTHESIS PROTEIN MEND FROM IN COMPLEX WITH OXOGLUTARATE ESCHERICHIA COLI K-12 MENAQUINONE THDP MG VITAMIN K2 CARBOXYLASE MAGNESIUM MMENAQUINONE BIOSYNTHESIS METAL-BINDING THIAMINE PYROPHOSPTRANSFERASE
Ref.: STRUCTURAL AND FUNCTIONAL ANALYSIS OF VITAMIN K2 SY PROTEIN MEND. BIOCHEM.BIOPHYS.RES.COMMUN. V. 388 748 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:557;
D:557;
Valid;
Valid;
none;
none;
Kd = 75 nM
146.098 C5 H6 O5 C(CC(...
CL A:563;
D:568;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
GOL A:577;
A:579;
A:580;
D:569;
D:571;
D:581;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:558;
D:558;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
NA A:559;
A:560;
A:561;
A:562;
A:564;
A:565;
A:566;
A:567;
A:568;
A:569;
A:570;
A:571;
A:572;
A:573;
A:574;
A:575;
A:576;
A:578;
D:559;
D:560;
D:561;
D:562;
D:563;
D:564;
D:565;
D:566;
D:567;
D:570;
D:572;
D:573;
D:574;
D:575;
D:576;
D:577;
D:578;
D:579;
D:580;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3HWW 1.95 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF MENAQUINONE SYNTHESIS PROTEIN MEND FROM IN COMPLEX WITH OXOGLUTARATE ESCHERICHIA COLI K-12 MENAQUINONE THDP MG VITAMIN K2 CARBOXYLASE MAGNESIUM MMENAQUINONE BIOSYNTHESIS METAL-BINDING THIAMINE PYROPHOSPTRANSFERASE
Ref.: STRUCTURAL AND FUNCTIONAL ANALYSIS OF VITAMIN K2 SY PROTEIN MEND. BIOCHEM.BIOPHYS.RES.COMMUN. V. 388 748 2009
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5EJ9 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5EJ5 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
3 5EJ4 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
4 5EJ7 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
5 5Z2R - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
6 5EJ6 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
7 5EJA - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
8 5EJ8 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
9 2JLC - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 5Z2P - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
11 3HWW Kd = 75 nM AKG C5 H6 O5 C(CC(=O)O)....
12 5Z2U - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5EJ9 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5EJ5 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
3 5EJ4 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
4 5EJ7 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
5 5Z2R - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
6 5EJ6 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
7 5EJA - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
8 5EJ8 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
9 2JLC - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 5Z2P - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
11 3HWW Kd = 75 nM AKG C5 H6 O5 C(CC(=O)O)....
12 5Z2U - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5EJ9 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5EJ5 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
3 5EJ4 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
4 5EJ7 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
5 5Z2R - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
6 5EJ6 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
7 5EJA - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
8 5EJ8 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
9 2JLC - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 5Z2P - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
11 3HWW Kd = 75 nM AKG C5 H6 O5 C(CC(=O)O)....
12 5Z2U - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 SIN 0.526316 0.833333
3 OOG 0.5 0.947368
4 69O 0.458333 0.714286
5 2IT 0.423077 0.615385
6 SHF 0.416667 0.666667
7 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HWW; Ligand: AKG; 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: 3hww.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3HWW; Ligand: AKG; 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: 3hww.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
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