Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:406;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
RI2 B:401;
A:401;
C:401;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 10 uM
310.09 C5 H12 O11 P2 C([C@...
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+]
MRD A:404;
 Invalid;
 none;
 submit data
118.174 C6 H14 O2 C[C@H...
PEG A:405;
B:404;
 Invalid;
Invalid;
 none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
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: RI2; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 RI2 1 1
2 PPC 0.695652 0.906977
3 PRP 0.695652 0.975
4 G16 0.666667 0.860465
5 R1P 0.609756 0.926829
6 AHG 0.575 0.926829
7 ABF 0.534884 0.95
8 HSX 0.534884 0.95
9 RP5 0.534884 0.95
10 XGP 0.533333 0.837209
11 G1P 0.533333 0.837209
12 M1P 0.533333 0.837209
13 GL1 0.533333 0.837209
14 JV4 0.521739 0.795455
15 GRF 0.511111 0.72549
16 A6P 0.5 0.857143
17 G6P 0.5 0.857143
18 M6D 0.5 0.857143
19 BG6 0.5 0.857143
20 M6P 0.5 0.857143
21 BGP 0.5 0.857143
22 FDQ 0.479167 0.904762
23 RF5 0.468085 0.840909
24 50A 0.468085 0.840909
25 GLP 0.46 0.72
26 4R1 0.46 0.72
27 NNG 0.444444 0.685185
28 D6G 0.44 0.818182
29 16G 0.436364 0.685185
30 4QY 0.436364 0.685185
31 BMX 0.436364 0.685185
32 GFP 0.411765 0.765957
33 GMB 0.410714 0.860465
34 GLC G6P 0.410714 0.723404
Similar Ligands (3D)
Ligand no: 1; Ligand: RI2; Similar ligands found: 36
No: Ligand Similarity coefficient
1 RUB 0.9603
2 IR8 0.9489
3 FBP 0.9131
4 IRN 0.9069
5 GAR 0.9035
6 XBP 0.8994
7 SGN 0.8958
8 AFP 0.8938
9 AIR 0.8921
10 IR9 0.8907
11 BSV 0.8887
12 D8X 0.8865
13 GUS 0.8859
14 HKK 0.8791
15 LG6 0.8764
16 LF5 0.8748
17 108 0.8744
18 JAA 0.8740
19 NGS 0.8738
20 HHB 0.8726
21 FZ6 0.8724
22 ET0 0.8664
23 UN3 0.8658
24 LNN 0.8624
25 6PG 0.8618
26 5KN 0.8617
27 I22 0.8615
28 F6R 0.8607
29 8RK 0.8602
30 G6Q 0.8593
31 JHY 0.8580
32 FDP 0.8578
33 AED 0.8570
34 60L 0.8532
35 ALA ZGL 0.8527
36 9X3 0.8518
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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