Receptor
PDB id Resolution Class Description Source Keywords
6CBO 1.6 Å EC: 2.-.-.- X-RAY STRUCTURE OF GENB1 FROM MICROMONOSPORA ECHINOSPORA IN WITH NEAMINE AND PLP (AS THE EXTERNAL ALDIMINE) MICROMONOSPORA ECHINOSPORA GENTAMICIN AMINOTRANSFERASE TRANSFERASE
Ref.: THE THREE-DIMENSIONAL STRUCTURE OF NEOB: AN AMINOTR INVOLVED IN THE BIOSYNTHESIS OF NEOMYCIN. PROTEIN SCI. V. 27 945 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 D:503;
D:504;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
DOW C:503;
D:502;
A:503;
B:503;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
553.501 C20 H36 N5 O11 P Cc1c(...
EDO A:502;
D:501;
B:502;
C:502;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MPO C:501;
A:501;
B:501;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
209.263 C7 H15 N O4 S C1COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5Z8A 1.4 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF GENB1 FROM MICROMONOSPORA ECHINOSPORA I WITH JI-20A AND PLP (EXTERNAL ALDIMINE) MICROMONOSPORA ECHINOSPORA AMINOTRANSFERASE PLP-BINDING TRANSFERASE
Ref.: COMPLETE RECONSTITUTION OF THE DIVERSE PATHWAYS OF GENTAMICIN B BIOSYNTHESIS. NAT. CHEM. BIOL. V. 15 295 2019
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 313 families.
1 5Z8A - PLP JIA n/a n/a
2 6CBO - DOW C20 H36 N5 O11 P Cc1c(c(c(c....
3 5Z8K - PLP XXX n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6CBO - DOW C20 H36 N5 O11 P Cc1c(c(c(c....
2 6CBN - OZY C31 H56 N7 O18 P Cc1c(c(c(c....
3 6CBK - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
4 6CBL - DOW C20 H36 N5 O11 P Cc1c(c(c(c....
5 6CBM - OZY C31 H56 N7 O18 P Cc1c(c(c(c....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5Z8A - PLP JIA n/a n/a
2 6CBO - DOW C20 H36 N5 O11 P Cc1c(c(c(c....
3 5Z8K - PLP XXX n/a n/a
4 6CBN - OZY C31 H56 N7 O18 P Cc1c(c(c(c....
5 6CBK - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
6 6CBL - DOW C20 H36 N5 O11 P Cc1c(c(c(c....
7 6CBM - OZY C31 H56 N7 O18 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DOW; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 DOW 1 1
2 OZY 0.698276 0.970588
3 9YM 0.462264 0.924242
4 PLG 0.434343 0.838235
5 DCS 0.433962 0.792208
6 33P 0.431373 0.782609
7 XXX 0.416667 0.636364
8 PMH 0.413462 0.776316
9 PL2 0.407407 0.767123
10 IK2 0.403846 0.802817
11 EA5 0.4 0.830986
Similar Ligands (3D)
Ligand no: 1; Ligand: DOW; Similar ligands found: 1
No: Ligand Similarity coefficient
1 PLP XXX 0.9908
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5Z8A; Ligand: PLP JIA; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 5z8a.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 3A8U PLP 6.40732
2 4ADC PLP 30.6636
Pocket No.: 2; Query (leader) PDB : 5Z8A; Ligand: PLP JIA; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 5z8a.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 3A8U PLP 6.40732
2 6S4G PMP 24.714
3 4ADC PLP 30.6636
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