Receptor
PDB id Resolution Class Description Source Keywords
5VKB 1.14 Å NON-ENZYME: OTHER ETHYLENE FORMING ENZYME IN COMPLEX WITH MANGANESE, 2-OXOGLUT ARGININAMIDE PSEUDOMONAS SAVASTANOI PV. PHASEOLICOLORGANISM_TAXID: 319 2-OXOGLUTARATE ARGININAMIDE OXIDOREDUCTASE
Ref.: STRUCTURES AND MECHANISMS OF THE NON-HEME FE(II)- A 2-OXOGLUTARATE-DEPENDENT ETHYLENE-FORMING ENZYME: S BINDING CREATES A TWIST. J. AM. CHEM. SOC. V. 139 11980 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:401;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
AAR A:403;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
174.224 C6 H16 N5 O C(C[C...
AKG A:402;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LUN 1.08 Å NON-ENZYME: OTHER ETHYLENE FORMING ENZYME FROM PSEUDOMONAS SYRINGAE PV. PHASEO P1 ULTRA-HIGH RESOLUTION CRYSTAL FORM IN COMPLEX WITH IRON,O XALYLGLYCINE AND ARGININE PSEUDOMONAS SAVASTANOI PV. PHASEOLICOLORGANISM_TAXID: 319 2-OXOGLUTARATE AND FERROUS IRON DEPENDENT OXYGENASE ETHYLENFORMING DOUBLE STRANDED BETA HELIX OXIDOREDUCTASE
Ref.: STRUCTURAL AND STEREOELECTRONIC INSIGHTS INTO OXYGENASE-CATALYZED FORMATION OF ETHYLENE FROM 2-OXOGLUTARATE. PROC. NATL. ACAD. SCI. V. 114 4667 2017 U.S.A.
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5V32 - MLT C4 H6 O5 C([C@H](C(....
2 5VKA - AKG C5 H6 O5 C(CC(=O)O)....
3 5V2T - TLA C4 H6 O6 [C@@H]([C@....
4 5VKB - AAR C6 H16 N5 O C(C[C@@H](....
5 5V31 - ARG C6 H15 N4 O2 C(C[C@@H](....
6 5V2X - AKG C5 H6 O5 C(CC(=O)O)....
7 5LUN - OGA C4 H5 N O5 C(C(=O)O)N....
8 5V2Y - ARG C6 H15 N4 O2 C(C[C@@H](....
9 5V2Z - ARG C6 H15 N4 O2 C(C[C@@H](....
10 5V34 - ARG C6 H15 N4 O2 C(C[C@@H](....
11 5MOF - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5V32 - MLT C4 H6 O5 C([C@H](C(....
2 5VKA - AKG C5 H6 O5 C(CC(=O)O)....
3 5V2T - TLA C4 H6 O6 [C@@H]([C@....
4 5VKB - AAR C6 H16 N5 O C(C[C@@H](....
5 5V31 - ARG C6 H15 N4 O2 C(C[C@@H](....
6 5V2X - AKG C5 H6 O5 C(CC(=O)O)....
7 5LUN - OGA C4 H5 N O5 C(C(=O)O)N....
8 5V2Y - ARG C6 H15 N4 O2 C(C[C@@H](....
9 5V2Z - ARG C6 H15 N4 O2 C(C[C@@H](....
10 5V34 - ARG C6 H15 N4 O2 C(C[C@@H](....
11 5MOF - AKG C5 H6 O5 C(CC(=O)O)....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5V32 - MLT C4 H6 O5 C([C@H](C(....
2 5VKA - AKG C5 H6 O5 C(CC(=O)O)....
3 5V2T - TLA C4 H6 O6 [C@@H]([C@....
4 5VKB - AAR C6 H16 N5 O C(C[C@@H](....
5 5V31 - ARG C6 H15 N4 O2 C(C[C@@H](....
6 5V2X - AKG C5 H6 O5 C(CC(=O)O)....
7 5LUN - OGA C4 H5 N O5 C(C(=O)O)N....
8 5V2Y - ARG C6 H15 N4 O2 C(C[C@@H](....
9 5V2Z - ARG C6 H15 N4 O2 C(C[C@@H](....
10 5V34 - ARG C6 H15 N4 O2 C(C[C@@H](....
11 5MOF - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AAR; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 AAR 1 1
2 DAR 0.705882 0.783784
3 ARG 0.705882 0.783784
4 CIR 0.540541 0.675
5 LYS ARG LYS ARG LYS ARG LYS ARG 0.487179 0.848485
6 ILO 0.418605 0.609756
7 3AR 0.413043 0.707317
8 LYN 0.405405 0.764706
9 2YH 0.404255 0.65
10 VIO 0.404255 0.604651
11 HAR 0.4 0.622222
12 4JK 0.4 0.619048
13 PG3 0.4 0.666667
14 ALA ARG 0.4 0.825
15 VUR 0.4 0.634146
16 NMM 0.4 0.7
Ligand no: 2; 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 : 5LUN; Ligand: ARG; 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: 5lun.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5LUN; Ligand: OGA; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 5lun.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5O9W AKG 24.7159
2 5C3R HMU 34.1108
3 5C3R AKG 34.1108
Pocket No.: 3; Query (leader) PDB : 5LUN; Ligand: OGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5lun.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5LUN; Ligand: ARG; Similar sites found with APoc: 1
This union binding pocket(no: 4) in the query (biounit: 5lun.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5O9W AKG 24.7159
Pocket No.: 5; Query (leader) PDB : 5LUN; Ligand: ARG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5lun.bio4) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5LUN; Ligand: OGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5lun.bio4) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5LUN; Ligand: OGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5lun.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5LUN; Ligand: ARG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5lun.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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