Receptor
PDB id Resolution Class Description Source Keywords
5YG6 2.35 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 AND GMP 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
G A:405;
B:404;
B:403;
A:404;
A:406;
 Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
 submit data
363.221 C10 H14 N5 O8 P c1nc2...
RI2 B:401;
A:401;
C:401;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 13.8 uM
310.09 C5 H12 O11 P2 C([C@...
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+]
MPD A:403;
 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: G; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GDP BEF 0.743902 0.947368
18 GTP MG 0.73494 0.972973
19 GMP 0.732394 0.866667
20 GPG 0.724138 0.948052
21 G2R 0.712644 0.948052
22 GDP ALF 0.701149 0.9
23 GDP AF3 0.701149 0.9
24 GKE 0.692308 0.948052
25 GDC 0.692308 0.948052
26 Y9Z 0.692308 0.890244
27 GDD 0.692308 0.948052
28 YGP 0.681319 0.9125
29 G3A 0.677419 0.960526
30 G5P 0.670213 0.960526
31 KB7 0.666667 0.8375
32 GFB 0.666667 0.948052
33 GDR 0.666667 0.948052
34 GTG 0.666667 0.924051
35 6CK 0.659574 0.924051
36 3GP 0.65 0.959459
37 JB2 0.645833 0.948052
38 GKD 0.645833 0.948052
39 GDX 0.639175 0.960526
40 GPD 0.639175 0.9125
41 GDP 7MG 0.635417 0.923077
42 G3D 0.617977 0.972973
43 U2G 0.617647 0.924051
44 KBD 0.612903 0.8375
45 2GP 0.609756 0.946667
46 IMP 0.609756 0.972603
47 JB3 0.607843 0.935897
48 CG2 0.605769 0.924051
49 G4P 0.604396 0.972973
50 DG 0.60241 0.922078
51 DGP 0.60241 0.922078
52 NGD 0.601942 0.948052
53 FEG 0.601942 0.890244
54 ZGP 0.596154 0.879518
55 0O2 0.595745 0.972973
56 KBJ 0.587629 0.807229
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 MD1 0.5625 0.879518
63 PGD 0.5625 0.9125
64 P2G 0.55814 0.894737
65 FE9 0.553571 0.784946
66 P1G 0.545455 0.883117
67 GH3 0.542553 0.96
68 I2C FE2 CMO CMO 0.539823 0.818182
69 TPG 0.53913 0.829545
70 GPX 0.53125 0.933333
71 DGI 0.527473 0.910256
72 G1R G1R 0.525862 0.911392
73 PGD O 0.521368 0.83908
74 DGT 0.521277 0.910256
75 G4M 0.520325 0.869048
76 AKW 0.513761 0.878049
77 G C 0.513514 0.911392
78 93A 0.511364 0.821429
79 IDP 0.505495 0.959459
80 MGQ 0.505155 0.948052
81 C2R 0.5 0.893333
82 A 0.5 0.905405
83 BGO 0.5 0.911392
84 AMZ 0.5 0.905405
85 AMP 0.5 0.905405
86 AIR 0.493671 0.890411
87 MGV 0.49 0.901235
88 QBQ 0.489362 0.972973
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 GGM 0.473684 0.888889
93 71V 0.47191 0.85
94 R5I 0.46875 0.933333
95 MGP 0.46875 0.948052
96 R7I 0.46875 0.933333
97 C2E 0.468085 0.933333
98 PCG 0.468085 0.945946
99 35G 0.468085 0.945946
100 G1G 0.466102 0.9125
101 7RA 0.465909 0.918919
102 FAI 0.465909 0.905405
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 1RB 0.465116 0.824324
106 6G0 0.463918 0.948052
107 5GP 5GP 0.463158 0.894737
108 RBZ 0.45977 0.815789
109 UCG 0.459016 0.923077
110 APC G U 0.458333 0.897436
111 IMO 0.449438 0.866667
112 6MZ 0.444444 0.868421
113 IRN 0.443038 0.808219
114 PMO 0.43956 0.792208
115 7RP 0.438202 0.864865
116 NYZ 0.4375 0.923077
117 GTA 0.436364 0.924051
118 JLN 0.433333 0.88
119 P2P 0.433333 0.842105
120 CZF 0.43299 0.92
121 XMP 0.428571 0.907895
122 M7G A2M G 0.427586 0.818182
123 PGS 0.425532 0.804878
124 RVP 0.423529 0.84
125 G2Q 0.423077 0.948052
126 ADP 0.419355 0.906667
127 ABM 0.417582 0.857143
128 45A 0.417582 0.857143
129 A2D 0.417582 0.881579
130 PRT 0.416667 0.945946
131 GUO 0.415842 0.932432
132 AT4 0.414894 0.871795
133 AMP MG 0.411111 0.866667
134 CA0 0.410526 0.883117
135 2SA 0.41 0.871795
136 OK8 0.41 0.87013
137 1YD 0.409091 0.933333
138 4BW 0.409091 0.933333
139 BA3 0.408602 0.881579
140 AP2 0.408602 0.871795
141 A12 0.408602 0.871795
142 6C6 0.408163 0.825
143 25A 0.407767 0.906667
144 NOS 0.406977 0.813333
145 ATP 0.40625 0.906667
146 KG4 0.40625 0.883117
147 HEJ 0.40625 0.906667
148 B4P 0.404255 0.881579
149 AP5 0.404255 0.881579
150 6IA 0.40404 0.785714
151 ACQ 0.40404 0.883117
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 3ZE 0.402062 0.871795
155 5FA 0.402062 0.906667
156 APC 0.402062 0.871795
157 AQP 0.402062 0.906667
158 AN2 0.4 0.894737
159 N6P 0.4 0.853333
Ligand no: 2; 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: G; Similar ligands found: 130
No: Ligand Similarity coefficient
1 IMU 0.9873
2 EO7 0.9741
3 IRP 0.9705
4 6OG 0.9662
5 FMP 0.9644
6 LMS 0.9642
7 5HM 0.9627
8 SRA 0.9580
9 D5M 0.9554
10 DI 0.9544
11 6CG 0.9535
12 AS 0.9519
13 DA 0.9516
14 8BR 0.9516
15 TMP 0.9439
16 8OG 0.9429
17 8GM 0.9380
18 6MA 0.9364
19 5HU 0.9359
20 NMN 0.9355
21 AOC 0.9351
22 8OP 0.9324
23 BRU 0.9319
24 NCN 0.9315
25 N5O 0.9301
26 A3N 0.9301
27 5AS 0.9293
28 Z8B 0.9277
29 ZAS 0.9253
30 3DH 0.9245
31 TKW 0.9226
32 5CM 0.9226
33 CNU 0.9219
34 U5P 0.9216
35 UFP 0.9213
36 5FU 0.9202
37 FDM 0.9196
38 MTA 0.9186
39 PFU 0.9182
40 BVP 0.9181
41 NEC 0.9166
42 J7C 0.9161
43 6RE 0.9161
44 5BU 0.9135
45 NYM 0.9128
46 7D5 0.9128
47 C 0.9124
48 BMQ 0.9115
49 BMP 0.9114
50 C5P 0.9107
51 FNU 0.9092
52 16B 0.9080
53 3F5 0.9079
54 UP6 0.9069
55 5IU 0.9044
56 MCF 0.9029
57 O8M 0.9028
58 QBT 0.9007
59 NUP 0.9005
60 CMP 0.9005
61 PRX 0.9002
62 UMP 0.9002
63 2DT 0.8989
64 D4M 0.8976
65 H2U 0.8976
66 ATM 0.8950
67 MZP 0.8948
68 DCM 0.8923
69 U 0.8917
70 9L3 0.8909
71 UMC 0.8908
72 NWQ 0.8908
73 DSH 0.8891
74 PSU 0.8885
75 EP4 0.8883
76 T3S 0.8881
77 SP1 0.8863
78 CH 0.8861
79 FN5 0.8861
80 M7G 0.8859
81 S5P 0.8854
82 4X2 0.8849
83 ADX 0.8846
84 M33 0.8835
85 6CN 0.8830
86 6AU 0.8828
87 GJV 0.8826
88 DU 0.8822
89 DUS 0.8821
90 OMP 0.8819
91 JW5 0.8800
92 9PP 0.8796
93 DDN 0.8785
94 TXS 0.8768
95 GNG 0.8759
96 A4D 0.8757
97 U6M 0.8756
98 T3P 0.8746
99 IXF 0.8739
100 A3P 0.8736
101 O7E 0.8733
102 FMC 0.8731
103 DC 0.8725
104 CAR 0.8721
105 A2P 0.8718
106 ADN 0.8712
107 6SW 0.8707
108 CL9 0.8698
109 2FA 0.8696
110 RP1 0.8682
111 2OM 0.8678
112 A8M 0.8659
113 M16 0.8655
114 43J 0.8654
115 MG7 0.8651
116 581 0.8650
117 MTE 0.8647
118 DOC 0.8630
119 43H 0.8607
120 NWW 0.8594
121 DBM 0.8588
122 3BH 0.8569
123 AJ8 0.8565
124 5CD 0.8557
125 5N5 0.8548
126 GAP 0.8544
127 6SX 0.8537
128 DAT 0.8522
129 RFZ 0.8517
130 1BJ 0.8511
Ligand no: 2; 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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