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Receptor
PDB id Resolution Class Description Source Keywords
4EAR 1.7 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE (W16Y, W178Y, H257W) MUTANT FROM HUMAN COMPLEXED WITH DADME-IMMG AP HOSPHATE HOMO SAPIENS PNPIMMUCILLIN PURINE NUCLEOSIDE PHOSPHORYLASE NUCLEOSIDE PURINE BASE BINDING PURINE-NUCLEOSIDE PHOSPHORYLASE ACTIVIBINDING TRANSFERASE ACTIVITY TRANSFERRING GLYCOSYL GROUPSPHOSPHATE ION BINDING CYTOSOL 6-FLUORO-L-TRYPTOPHAN TRANTRANSFERASE INHIBITOR COMPLEX
Ref.: CATALYTIC SITE CONFORMATIONS IN HUMAN PNP BY (19)F-CRYSTALLOGRAPHY. CHEM.BIOL. V. 20 212 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:302;
C:302;
B:302;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
IM5 B:301;
C:301;
A:301;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
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 17 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 H17 N4 O3 c1c(c2c([n....
3 1RR6 - IMH C11 H14 N4 O4 c1c(c2c([n....
4 2A0X Ki = 950 pM DIH C12 H17 N4 O3 c1c(c2c([n....
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 H17 N4 O3 c1c(c2c([n....
9 1RSZ - DIH C12 H17 N4 O3 c1c(c2c([n....
10 2A0W Ki = 270 pM DIH C12 H17 N4 O3 c1c(c2c([n....
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 (44)
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 H17 N4 O3 c1c(c2c([n....
3 1RR6 - IMH C11 H14 N4 O4 c1c(c2c([n....
4 2A0X Ki = 950 pM DIH C12 H17 N4 O3 c1c(c2c([n....
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 H17 N4 O3 c1c(c2c([n....
9 1RSZ - DIH C12 H17 N4 O3 c1c(c2c([n....
10 2A0W Ki = 270 pM DIH C12 H17 N4 O3 c1c(c2c([n....
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 5TBT - CTN C9 H13 N3 O5 C1=CN(C(=O....
30 5TBU - HPA C5 H4 N4 O c1[nH]c2c(....
31 5TBS - ADE C5 H5 N5 c1[nH]c2c(....
32 4EAR - IM5 C12 H17 N5 O3 c1c(c2c([n....
33 5ETJ Kd = 66 pM IM5 C12 H17 N5 O3 c1c(c2c([n....
34 4EB8 - IM5 C12 H17 N5 O3 c1c(c2c([n....
35 2P4S Kd = 0.42 nM DIH C12 H17 N4 O3 c1c(c2c([n....
36 3FB1 - R1P C5 H11 O8 P C([C@@H]1[....
37 3E9R - ADE C5 H5 N5 c1[nH]c2c(....
38 3E0Q - JFD C4 H4 Br N3 O2 C1(=C(NC(=....
39 3FNQ - HPA C5 H4 N4 O c1[nH]c2c(....
40 3FAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
41 3IEX - GMP C10 H13 N5 O5 c1nc2c(n1[....
42 3DJF ic50 = 0.8 uM BC3 C12 H11 N5 O c1cc(cnc1)....
43 3F8W - ADN C10 H13 N5 O4 c1nc(c2c(n....
44 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 with APoc: 59
This union binding pocket(no: 1) in the query (biounit: 5etj.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 2RDE C2E 1.59363
2 6E1Q CFA 1.85185
3 3ITA AIC 2.16049
4 4FK7 P34 2.18341
5 2C5S AMP 2.42131
6 3WXO NIZ 2.46914
7 1RJW ETF 2.77778
8 1Q8O MAN MMA 2.77778
9 5YJS SAL 3.08642
10 6ACS CIT 3.10078
11 6BSX E7S 3.37079
12 4TXJ THM 3.37838
13 1Q8A HCS 3.39506
14 4QAR ADE 3.48259
15 4ZV1 ARG 3.86266
16 5W75 SUC 4.01235
17 2IVD ACJ 4.01235
18 3LGS ADE 4.11985
19 3LGS SAH 4.11985
20 3EUF BAU 4.32099
21 3CBC DBS 4.54545
22 3A16 PXO 4.93827
23 5L2R MLA 4.93827
24 5NCB JZ3 4.93827
25 2C3H GLC GLC 5.10204
26 2Y7I ARG 5.24017
27 5TQZ GLC 5.33333
28 2XZ9 PYR 5.55556
29 4BMX ADE 5.57769
30 3P0F BAU 5.72391
31 4FFS BIG 5.85774
32 1JE1 GMP 5.9322
33 6C5F 7L9 5.98291
34 1MFI FHC 6.14035
35 3BJE URA 6.17284
36 6GMR F4K 6.18557
37 2Q89 6CS 6.22568
38 3N8K D1X 6.39535
39 3KVY URA 6.47249
40 4WKC BIG 6.93878
41 1GPM AMP 7.09877
42 5YSI NCA 7.23684
43 4WKB TDI 7.37705
44 1ODJ GMP 7.65957
45 4YJK URA 7.93651
46 1T9D P22 8.95062
47 5AZC PGT 9.33333
48 5O0J GLC 9.5679
49 1ZOS MTM 11.3043
50 4BWL MN9 11.8421
51 3ZF8 GDP 12.459
52 3BL6 FMC 18.2609
53 3QPB URA 20.2128
54 6AYR BIG 25.2101
55 4GLJ RHB 31.3131
56 5F7J ADE 33.0247
57 2A8Y MTA 38.8889
58 1C3X 8IG 43.2331
59 1K27 MTM 43.4629
Pocket No.: 2; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 5etj.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 5CLO NS8 None
2 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 1.54321
3 1LOP SIN ALA PRO ALA NIT 1.82927
4 3FAX BGC GLC GLC 2.16049
5 5EOO CIT 2.64151
6 5J75 6GQ 3.0303
7 3BOF HCS 3.39506
8 5WS9 OXL 4.32099
9 1KAH HIS 7.09877
10 3JDW ORN 7.80142
Pocket No.: 3; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found with APoc: 11
This union binding pocket(no: 3) in the query (biounit: 5etj.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 1RZX ACE VAL LYS GLU SER LEU VAL None
2 5HGZ MLA 2.05761
3 3VSE SAH 2.16049
4 2VNO GAL GAL FUC 2.77778
5 2VAR AMP 2.8754
6 4YRD 3IT 3.06407
7 4RF7 ARG 3.08642
8 6AYU F6P 3.7037
9 3NBC LAT 4.05405
10 3CL7 HYN 5.84416
11 5EZU MYR 6.74157
Pocket No.: 4; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found with APoc: 36
This union binding pocket(no: 4) in the query (biounit: 5etj.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3RJ5 NAD 1.5748
2 3R9V DXC 1.74825
3 1J0D 5PA 2.16049
4 1CT9 GLN 2.16049
5 3ZV6 4HB 2.4911
6 3ESS 18N 3.04348
7 2OQ2 A3P 3.08642
8 6BQC LOP 3.39506
9 6GAS FAD 3.62538
10 1TLG GAL 4
11 5XOY LYS 4.01235
12 4B2Z P5S 4.32099
13 3SZB I1E 4.32099
14 3O0Q ADN 4.62963
15 3O0Q TTP 4.62963
16 3O0Q GDP 4.62963
17 2ZXI FAD 4.62963
18 3FSM 2NC 4.92611
19 2AE2 PTO 4.93827
20 3LZW NAP 4.93827
21 4WHZ 3NL 5.55556
22 3HB5 NAP 6.11621
23 3EYA TDP 6.17284
24 4YUW 4JU 6.57895
25 5MW4 5JU 7.09877
26 4XIZ LPP 7.14286
27 2O1C PPV 7.33333
28 4Z3X 4KX 7.40741
29 4Z3X MTE 7.40741
30 3EWC MCF 7.54717
31 3PA8 621 8.26772
32 5C8W PCG 8.39161
33 5CKS GAL 8.64198
34 1U1F 183 10.1562
35 4NJS G08 11.1111
36 3NTD COA 11.4198
Pocket No.: 5; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found with APoc: 13
This union binding pocket(no: 5) in the query (biounit: 5etj.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5U3F 7TS 1.54321
2 5O4J 9KH 1.82482
3 5O4J SAH 1.82482
4 1A59 CIT 2.1164
5 1F0X FAD 2.16049
6 1KOR ARG 2.77778
7 4PFW MAN MAN BMA BMA BMA BMA 3.08642
8 5A7Y SAH 3.20513
9 3KA2 2NC 4.92611
10 2X1L MET 5.55556
11 1NZY BCA 6.3197
12 3KO0 TFP 7.92079
13 5W97 CHD 15.5963
Pocket No.: 6; Query (leader) PDB : 5ETJ; Ligand: IM5; Similar sites found with APoc: 18
This union binding pocket(no: 6) in the query (biounit: 5etj.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5Z2L NDP 1.63265
2 5O4J PJL 1.82482
3 1Q9I TEO 2.46914
4 1Q9I FAD 2.46914
5 2E5V FAD 2.46914
6 1KOR ANP 2.77778
7 2P3C 3TL 3.0303
8 5G6U TRP 3.83142
9 5X8G S0N 4.32099
10 5IH9 6BF 4.77612
11 3LZW FAD 4.93827
12 2HQM FAD 4.93827
13 1KQF MGD 5.24691
14 1KDK DHT 6.21469
15 5FFF 5XC 7.00389
16 6B2M COA 7.69231
17 3WCA FPS 7.71605
18 5T2Z 017 12.1212
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