Receptor
PDB id Resolution Class Description Source Keywords
5EJA 1.6 Å EC: 2.2.1.9 ECMEND-THDP-MN2+ COMPLEX SOAKED WITH 2-KETOGLUTARATE FOR 2 M SOAKED WITH ISOCHORISMATE FOR 7 MIN ESCHERICHIA COLI K12 POST-DECARBOXYLATION INTERMEDIATE TRANSFERASE
Ref.: A THIAMINE-DEPENDENT ENZYME UTILIZES AN ACTIVE TETR INTERMEDIATE IN VITAMIN K BIOSYNTHESIS J.AM.CHEM.SOC. V. 138 7244 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN C:602;
F:602;
B:602;
G:602;
D:602;
A:602;
H:602;
E:602;
 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;
 submit data
54.938 Mn [Mn+2...
TD6 G:601;
C:601;
B:601;
E:601;
D:601;
F:601;
H:601;
A:601;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
527.403 C16 H25 N4 O10 P2 S Cc1c(...
GOL F:603;
E:603;
A:603;
D:603;
C:603;
B:603;
G:603;
H:603;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
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 (2D)
Ligand no: 1; Ligand: TD6; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 TD6 1 1
2 TD9 0.866667 1
3 TD8 0.866667 1
4 WWF 0.758242 0.935897
5 TDW 0.733333 0.947368
6 TOG 0.656566 1
7 HTL 0.625 0.960526
8 TDL 0.62 0.925
9 8PA 0.609091 0.923077
10 THV 0.59 0.935065
11 AUJ 0.584158 0.924051
12 THY 0.578431 0.923077
13 TDK 0.567308 0.9
14 5SR 0.554455 0.947368
15 O2T 0.552381 0.936709
16 T5X 0.544643 0.901235
17 T6F 0.544643 0.901235
18 THW 0.542056 0.935065
19 TPP 0.540816 0.921053
20 D7K 0.517544 0.888889
21 S1T 0.504854 0.842105
22 R1T 0.504854 0.842105
23 V4E 0.504854 0.921053
24 1U0 0.490566 0.822785
25 TPW 0.48 0.828947
26 PYI 0.466019 0.818182
27 TDP 0.457143 0.907895
28 TPS 0.425743 0.881579
29 8EO 0.420561 0.851852
30 2TP 0.416667 0.886076
31 NDQ 0.416667 0.843373
32 TMV 0.416667 0.884615
33 ZP1 0.414634 0.891566
34 TD7 0.413793 0.925
35 TPU 0.413462 0.780488
36 QSP 0.408333 0.902439
37 8FL 0.407407 0.829268
38 G8G 0.40566 0.790123
39 TDP DX5 0.403226 0.876543
Similar Ligands (3D)
Ligand no: 1; Ligand: TD6; Similar ligands found: 5
No: Ligand Similarity coefficient
1 TDP COI 0.9198
2 8N9 0.8813
3 THD 0.8719
4 TPP PYR 0.8671
5 TDM 0.8554
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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