Receptor
PDB id Resolution Class Description Source Keywords
5ETJ 2.3 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE (E258D, MUTANT FROM HUMAN COMPLEXED WITH DADME-IMMG AND PHOSPHATE HOMO SAPIENS PHOSPHORYLASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: MODULATING ENZYME CATALYSIS THROUGH MUTATIONS DESIG ALTER RAPID PROTEIN DYNAMICS. J.AM.CHEM.SOC. V. 138 3403 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:303;
A:302;
C:302;
B:302;
D:303;
F:304;
C:303;
F:303;
B:303;
E:302;
D:302;
F:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
IM5 A:301;
C:301;
B:301;
E:301;
F:302;
D:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 66 pM
279.295 C12 H17 N5 O3 c1c(c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ETJ 2.3 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE (E258D, MUTANT FROM HUMAN COMPLEXED WITH DADME-IMMG AND PHOSPHATE HOMO SAPIENS PHOSPHORYLASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: MODULATING ENZYME CATALYSIS THROUGH MUTATIONS DESIG ALTER RAPID PROTEIN DYNAMICS. J.AM.CHEM.SOC. V. 138 3403 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 4EAR - IM5 C12 H17 N5 O3 c1c(c2c([n....
2 5ETJ Kd = 66 pM IM5 C12 H17 N5 O3 c1c(c2c([n....
3 4EB8 - IM5 C12 H17 N5 O3 c1c(c2c([n....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2ON6 Ki = 172 nM IMH C11 H14 N4 O4 c1c(c2c([n....
2 2A0Y Ki = 900 pM DIH C12 H19 N4 O3 C1[C@@H]([....
3 1RR6 - IMH C11 H14 N4 O4 c1c(c2c([n....
4 2A0X Ki = 950 pM DIH C12 H19 N4 O3 C1[C@@H]([....
5 3GB9 - A2F C5 H4 F N5 c1[nH]c2c(....
6 1RT9 - IMH C11 H14 N4 O4 c1c(c2c([n....
7 5UGF - IM5 C12 H17 N5 O3 c1c(c2c([n....
8 3BGS Ki = 380 pM DIH C12 H19 N4 O3 C1[C@@H]([....
9 1RSZ - DIH C12 H19 N4 O3 C1[C@@H]([....
10 2A0W Ki = 270 pM DIH C12 H19 N4 O3 C1[C@@H]([....
11 1B8O Ki = 23 pM IMH C11 H14 N4 O4 c1c(c2c([n....
12 1A9T - R1P C5 H11 O8 P C([C@@H]1[....
13 1VFN Ki = 2.5 uM HPA C5 H4 N4 O c1[nH]c2c(....
14 2QPL ic50 = 18.9 uM BTY C6 H7 N5 O Cc1cc2n(n1....
15 2AI1 ic50 = 300 nM P1G C12 H16 N5 O8 P c1nc2c(n1[....
16 1B8N Ki = 30 pM IMG C11 H15 N5 O4 c1c(c2c([n....
17 1A9S - NOS C10 H12 N4 O5 c1nc2c(n1[....
18 2AI3 ic50 = 5000 nM P2G C11 H14 N5 O8 P c1nc2c(n1[....
19 1LVU Kd = 4.8 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
20 1A9P - 9DI C11 H13 N3 O5 c1c(c2c([n....
21 2AI2 ic50 = 30 nM P1D C13 H16 N3 O8 P c1c(c2c([n....
22 1V48 Ki = 16 nM HA1 C10 H14 F2 N5 O4 P c1nc2c(n1C....
23 1A9Q - HPA C5 H4 N4 O c1[nH]c2c(....
24 3FUC Kd = 190 pM 9D9 9DG n/a n/a
25 1A9R - HPA C5 H4 N4 O c1[nH]c2c(....
26 1LV8 Kd = 3.5 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
27 1FXU - GU7 C10 H16 N6 O3 c1nc2c(n1C....
28 4EAR - IM5 C12 H17 N5 O3 c1c(c2c([n....
29 5ETJ Kd = 66 pM IM5 C12 H17 N5 O3 c1c(c2c([n....
30 4EB8 - IM5 C12 H17 N5 O3 c1c(c2c([n....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ON6 Ki = 172 nM IMH C11 H14 N4 O4 c1c(c2c([n....
2 2A0Y Ki = 900 pM DIH C12 H19 N4 O3 C1[C@@H]([....
3 1RR6 - IMH C11 H14 N4 O4 c1c(c2c([n....
4 2A0X Ki = 950 pM DIH C12 H19 N4 O3 C1[C@@H]([....
5 3GB9 - A2F C5 H4 F N5 c1[nH]c2c(....
6 1RT9 - IMH C11 H14 N4 O4 c1c(c2c([n....
7 5UGF - IM5 C12 H17 N5 O3 c1c(c2c([n....
8 3BGS Ki = 380 pM DIH C12 H19 N4 O3 C1[C@@H]([....
9 1RSZ - DIH C12 H19 N4 O3 C1[C@@H]([....
10 2A0W Ki = 270 pM DIH C12 H19 N4 O3 C1[C@@H]([....
11 1B8O Ki = 23 pM IMH C11 H14 N4 O4 c1c(c2c([n....
12 1A9T - R1P C5 H11 O8 P C([C@@H]1[....
13 1VFN Ki = 2.5 uM HPA C5 H4 N4 O c1[nH]c2c(....
14 2QPL ic50 = 18.9 uM BTY C6 H7 N5 O Cc1cc2n(n1....
15 2AI1 ic50 = 300 nM P1G C12 H16 N5 O8 P c1nc2c(n1[....
16 1B8N Ki = 30 pM IMG C11 H15 N5 O4 c1c(c2c([n....
17 1A9S - NOS C10 H12 N4 O5 c1nc2c(n1[....
18 2AI3 ic50 = 5000 nM P2G C11 H14 N5 O8 P c1nc2c(n1[....
19 1LVU Kd = 4.8 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
20 1A9P - 9DI C11 H13 N3 O5 c1c(c2c([n....
21 2AI2 ic50 = 30 nM P1D C13 H16 N3 O8 P c1c(c2c([n....
22 1V48 Ki = 16 nM HA1 C10 H14 F2 N5 O4 P c1nc2c(n1C....
23 1A9Q - HPA C5 H4 N4 O c1[nH]c2c(....
24 3FUC Kd = 190 pM 9D9 9DG n/a n/a
25 1A9R - HPA C5 H4 N4 O c1[nH]c2c(....
26 1LV8 Kd = 3.5 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
27 1FXU - GU7 C10 H16 N6 O3 c1nc2c(n1C....
28 5IFK - HPA C5 H4 N4 O c1[nH]c2c(....
29 4EAR - IM5 C12 H17 N5 O3 c1c(c2c([n....
30 5ETJ Kd = 66 pM IM5 C12 H17 N5 O3 c1c(c2c([n....
31 4EB8 - IM5 C12 H17 N5 O3 c1c(c2c([n....
32 2P4S Kd = 0.42 nM DIH C12 H19 N4 O3 C1[C@@H]([....
33 3FB1 - R1P C5 H11 O8 P C([C@@H]1[....
34 3E9R - ADE C5 H5 N5 c1[nH]c2c(....
35 3E0Q - JFD C4 H4 Br N3 O2 C1(=C(NC(=....
36 3FNQ - HPA C5 H4 N4 O c1[nH]c2c(....
37 3FAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
38 3IEX - GMP C10 H13 N5 O5 c1nc2c(n1[....
39 3DJF ic50 = 0.8 uM BC3 C12 H11 N5 O c1cc(cnc1)....
40 3F8W - ADN C10 H13 N5 O4 c1nc(c2c(n....
41 1VMK - GUN C5 H5 N5 O c1[nH]c2c(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IM5; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 IM5 1 1
2 BC3 0.4125 0.657143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 5etj.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CLO NS8 0.0137 0.43533 None
2 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.01537 0.4426 1.54321
3 3ITA AIC 0.03376 0.42059 2.16049
4 4FK7 P34 0.02643 0.42763 2.18341
5 1Q8A HCS 0.03983 0.41111 3.39506
6 4QAR ADE 0.00002473 0.5558 3.48259
7 4ZV1 ARG 0.0426 0.40585 3.86266
8 2IVD ACJ 0.01919 0.41665 4.01235
9 3LGS SAH 0.00006503 0.51814 4.11985
10 3LGS ADE 0.00006503 0.51814 4.11985
11 3EUF BAU 0.00363 0.44892 4.32099
12 3A16 PXO 0.01867 0.43102 4.93827
13 5L2R MLA 0.03067 0.41346 4.93827
14 2Y7I ARG 0.02352 0.4158 5.24017
15 4WKB TDI 0.0004707 0.46982 7.37705
16 1ODJ GMP 0.00002943 0.55207 7.65957
17 5UDS ATP 0.03534 0.40654 7.69231
18 4YJK URA 0.0003305 0.52794 7.93651
19 1ZOS MTM 0.0001371 0.51351 11.3043
20 4BWL MN9 0.04794 0.40872 11.8421
21 5F7J ADE 0.0000004284 0.61211 33.0247
22 2A8Y MTA 0.00000003695 0.66046 38.8889
Pocket No.: 2; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5etj.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5etj.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found: 15
This union binding pocket(no: 4) in the query (biounit: 5etj.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ESS 18N 0.02433 0.4013 3.04348
2 2OQ2 A3P 0.01394 0.40043 3.08642
3 4TXJ THM 0.001141 0.46 3.37838
4 1TLG GAL 0.02106 0.41197 4
5 4BMX ADE 0.00002402 0.51783 5.57769
6 3BJE URA 0.000009683 0.45346 6.17284
7 3KVY URA 0.00007874 0.43945 6.47249
8 4XIZ LPP 0.01683 0.40717 7.14286
9 3PA8 621 0.01995 0.40182 8.26772
10 5CKS GAL 0.02442 0.40254 8.64198
11 1U1F 183 0.008082 0.4347 10.1562
12 3NTD COA 0.02431 0.40061 11.4198
13 3BL6 FMC 0.008627 0.43057 18.2609
14 3QPB URA 0.00004173 0.43617 20.2128
15 1C3X 8IG 0.00000009065 0.50549 43.2331
Pocket No.: 5; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5etj.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5etj.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback