Receptor
PDB id Resolution Class Description Source Keywords
5YFJ 2.2 Å EC: 5.3.1.29 CRYSTAL STRUCTURE OF RIBOSE-1,5-BISPHOSPHATE ISOMERASE FROM HORIKOSHII OT3 IN COMPLEX WITH RIBULOSE-1,5-BISPHOSPHATE PYROCOCCUS HORIKOSHII ISOMERASE NMP DEGRADATION PATHWAY RIBOSE-1 5-BISPHOSPHATEROSSMANN-LIKE FOLD
Ref.: A PRESUMED HOMOLOGUE OF THE REGULATORY SUBUNITS OF FUNCTIONS AS RIBOSE-1,5-BISPHOSPHATE ISOMERASE IN P HORIKOSHII OT3. SCI REP V. 8 1891 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:403;
C:403;
B:403;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
35.453 Cl [Cl-]
K B:402;
C:402;
A:402;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
39.098 K [K+]
RUB C:401;
A:401;
B:401;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
310.09 C5 H12 O11 P2 C([C@...
PEG A:404;
B:404;
 Invalid;
Invalid;
 none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
MPD A:405;
 Invalid;
 none;
 submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YFT 2.21 Å EC: 5.3.1.29 CRYSTAL STRUCTURE OF RIBOSE-1,5-BISPHOSPHATE ISOMERASE MUTAN FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH RIBOSE-1,5- B ISPHOSPHATE PYROCOCCUS HORIKOSHII ISOMERASE NMP DEGRADATION PATHWAY RIBOSE-1 5-BISPHOSPHATEROSSMANN-LIKE FOLD
Ref.: A PRESUMED HOMOLOGUE OF THE REGULATORY SUBUNITS OF FUNCTIONS AS RIBOSE-1,5-BISPHOSPHATE ISOMERASE IN P HORIKOSHII OT3. SCI REP V. 8 1891 2018
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5YFS Kd = 13.8 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
2 5YFT Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
3 5YFW Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
4 5YG7 Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
5 5YGA Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
6 5YFU - RUB C5 H12 O11 P2 C([C@H]([C....
7 5YG6 Kd = 13.8 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
8 5YFJ - RUB C5 H12 O11 P2 C([C@H]([C....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5YFS Kd = 13.8 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
2 5YFT Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
3 5YFW Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
4 5YG7 Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
5 5YGA Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
6 5YFU - RUB C5 H12 O11 P2 C([C@H]([C....
7 5YG6 Kd = 13.8 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
8 5YFJ - RUB C5 H12 O11 P2 C([C@H]([C....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5YFS Kd = 13.8 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
2 5YFT Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
3 5YFW Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
4 5YG7 Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
5 5YGA Kd = 10 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
6 5YFU - RUB C5 H12 O11 P2 C([C@H]([C....
7 5YG6 Kd = 13.8 uM RI2 C5 H12 O11 P2 C([C@@H]1[....
8 5YFJ - RUB C5 H12 O11 P2 C([C@H]([C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: RUB; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 XBP 1 1
2 RUB 1 1
3 5RP 0.657895 0.944444
4 HMS 0.657895 0.944444
5 5SP 0.657895 0.944444
6 P6F 0.634146 0.942857
7 P6T 0.634146 0.942857
8 2FP 0.634146 0.942857
9 DEZ 0.578947 0.888889
10 DER 0.578947 0.888889
11 DXP 0.564103 0.861111
12 MRU 0.55814 0.871795
13 RES 0.52381 0.666667
14 F6R 0.477273 0.916667
15 TG6 0.477273 0.916667
16 HG3 0.472222 0.828571
17 PA5 0.465116 0.888889
18 R10 0.465116 0.888889
19 I22 0.456522 0.916667
20 M2P 0.447368 0.914286
21 GOS 0.447368 0.914286
22 9C2 0.446809 0.653061
23 LG6 0.444444 0.888889
24 6PG 0.444444 0.888889
25 4TP 0.44186 0.744186
26 PAN 0.425532 0.666667
27 E4P 0.414634 0.911765
28 A5P 0.404762 0.888889
29 LXP 0.404762 0.888889
30 LX1 0.404762 0.810811
31 DX5 0.404762 0.888889
32 3PG 0.4 0.885714
Similar Ligands (3D)
Ligand no: 1; Ligand: RUB; Similar ligands found: 13
No: Ligand Similarity coefficient
1 RI2 0.9603
2 IR8 0.9220
3 XDP 0.9089
4 AFP 0.8918
5 PAZ 0.8883
6 AHG 0.8845
7 FBP 0.8839
8 IR9 0.8825
9 HZZ 0.8824
10 CAP 0.8822
11 GAR 0.8807
12 KOH 0.8623
13 KD0 0.8515
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5YFT; Ligand: RI2; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 5yft.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2YVK MRU 45.679
2 2YVK MRU 45.679
3 2YVK MRU 45.679
4 2YVK MRU 45.679
Pocket No.: 2; Query (leader) PDB : 5YFT; Ligand: RI2; 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: 5yft.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5YFT; Ligand: RI2; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 5yft.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2YVK MRU 45.679
2 2YVK MRU 45.679
3 2YVK MRU 45.679
4 2YVK MRU 45.679
Pocket No.: 4; Query (leader) PDB : 5YFT; Ligand: RI2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5yft.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5YFT; Ligand: RI2; Similar sites found with APoc: 4
This union binding pocket(no: 5) in the query (biounit: 5yft.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2YVK MRU 45.679
2 2YVK MRU 45.679
3 2YVK MRU 45.679
4 2YVK MRU 45.679
Pocket No.: 6; Query (leader) PDB : 5YFT; Ligand: RI2; 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: 5yft.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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