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 (9)
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 5EJ6 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
6 5EJA - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
7 5EJ8 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
8 2JLC - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
9 3HWW Kd = 75 nM AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (9)
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 5EJ6 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
6 5EJA - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
7 5EJ8 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
8 2JLC - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
9 3HWW Kd = 75 nM AKG C5 H6 O5 C(CC(=O)O)....
50% Homology Family (9)
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 5EJ6 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
6 5EJA - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
7 5EJ8 - TD6 C16 H25 N4 O10 P2 S Cc1c(sc([n....
8 2JLC - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
9 3HWW Kd = 75 nM AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 OOG 0.5 0.947368
3 69O 0.458333 0.714286
4 2IT 0.423077 0.615385
5 SHF 0.416667 0.666667
6 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: 36
This union binding pocket(no: 1) in the query (biounit: 3hww.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4X1Z FUC GAL NDG 0.01031 0.40513 1.80723
2 1D8C GLV 0.01207 0.40851 2.15827
3 2O1S TDP 0.004859 0.41025 2.51799
4 3B6C SDN 0.00907 0.41912 2.5641
5 1P7T PYR 0.02618 0.4052 2.69784
6 1PCA CIT 0.005614 0.40429 2.97767
7 4PPF FLC 0.003451 0.45082 3.42857
8 3FGZ BEF 0.01864 0.40315 3.90625
9 5FJJ MAN 0.001809 0.42705 4.13669
10 2QV7 ADP 0.00136 0.43477 4.1543
11 4KFU ACP 0.02547 0.40344 4.24528
12 4R2I ANP 0.01345 0.41049 4.28571
13 1QPB PYM 0.0002195 0.40872 4.4964
14 1QPB TPP 0.0002195 0.40872 4.4964
15 1ZPD DPX 0.00007729 0.51338 4.67626
16 2D2F ADP 0.03402 0.40063 5.2
17 2VK4 TPP 0.00008956 0.42444 6.11511
18 2OG2 MLI 0.009238 0.41141 6.12813
19 5TME UDP 0.008793 0.41062 6.20985
20 2IHT TPP 0.0006333 0.46567 6.47482
21 3EYA TDP 0.0001417 0.41692 7.10383
22 3B9Q MLI 0.01892 0.40319 7.28477
23 3A3B FMN 0.002422 0.44247 7.36842
24 3A3B RBF 0.002676 0.44035 7.36842
25 2PZE ATP 0.0194 0.40595 7.42358
26 2VBF TPP 0.00001531 0.54636 7.73381
27 2F5X ASP 0.01465 0.4109 8.01282
28 1YQT ADP 0.006018 0.43098 8.17844
29 4CPB GAL CN8 0.02688 0.40377 9.09091
30 1T9D P22 0.0001168 0.51406 9.35252
31 1JJ7 ADP 0.002312 0.46069 9.61539
32 2J5V PCA 0.0142 0.42606 9.80926
33 5E5U MLI 0.009277 0.43884 9.84848
34 4RJK TPP 0.0003177 0.40033 9.89209
35 1BXG NAD 0.0172 0.40049 10.1124
36 2UZ1 TPP 0.0001189 0.4183 11.6906
Pocket No.: 2; Query (leader) PDB : 3HWW; Ligand: AKG; 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: 3hww.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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