Receptor
PDB id Resolution Class Description Source Keywords
2JLC 2.5 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF E.COLI MEND, 2-SUCCINYL-5-ENOLPYRUVYL- 6-HYDROXY-3-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE - NATIVE P ROTEIN ESCHERICHIA COLI MENAQUINONE BIOSYNTHESIS MANGANESE TRANSFERASE THIAMINE DIPHOSPHATE COFACTOR THIAMINE PYROPHOSPHATE
Ref.: SPECIFICITY AND REACTIVITY IN MENAQUINONE BIOSYNTHESIS: THE STRUCTURE OF ESCHERICHIA COLI MEND (2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE). J.MOL.BIOL. V. 384 1353 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:602;
B:602;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
TPP A:601;
B:601;
Valid;
Valid;
none;
none;
submit data
425.314 C12 H19 N4 O7 P2 S Cc1c(...
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: TPP; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP 1 1
2 V4E 0.891892 1
3 TDP 0.84 0.985714
4 TPS 0.816901 0.957143
5 NDQ 0.769231 0.909091
6 TMV 0.769231 0.958333
7 2TP 0.725 0.932432
8 VNP 0.721519 0.958904
9 VIB 0.621622 0.75
10 PYI 0.581395 0.887324
11 HTL 0.566667 0.958904
12 TDW 0.566667 0.972222
13 AUJ 0.55914 0.921053
14 N1T 0.556818 0.985714
15 FTP 0.551724 0.835616
16 THV 0.548387 0.958904
17 TPW 0.546512 0.9
18 WWF 0.542553 0.933333
19 TD6 0.540816 0.921053
20 THY 0.536842 0.945946
21 TOG 0.536082 0.921053
22 TDL 0.53125 0.897436
23 THW 0.530612 0.958904
24 TD9 0.53 0.921053
25 TD8 0.53 0.921053
26 TDK 0.525773 0.921053
27 D7K 0.490566 0.909091
28 R1T 0.489362 0.887324
29 S1T 0.489362 0.887324
30 TPU 0.483146 0.842105
31 5SR 0.479167 0.945205
32 T6F 0.476636 0.897436
33 T5X 0.476636 0.897436
34 1U0 0.474227 0.84
35 8PA 0.459459 0.945946
36 8EO 0.457447 0.92
37 8FL 0.457447 0.894737
38 TZD 0.451613 0.883117
39 O2T 0.45098 0.909091
40 TDM 0.443299 0.894737
41 8EL 0.442105 0.894737
42 G8G 0.44086 0.805195
43 TDN 0.415842 0.871795
44 THD 0.411765 0.839506
45 8N9 0.411765 0.839506
46 MP5 0.407895 0.676056
47 TD7 0.40566 0.85
48 DPX 0.4 0.734177
Similar Ligands (3D)
Ligand no: 1; Ligand: TPP; Similar ligands found: 4
No: Ligand Similarity coefficient
1 8EF 0.9955
2 TP9 0.9752
3 HTD 0.9623
4 HE3 0.9027
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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