Receptor
PDB id Resolution Class Description Source Keywords
1ODJ 2.4 Å EC: 2.4.2.28 PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS THERMUS THERMOPHILUS TRANSFERASE NUCLEOSIDE PHOSPHORYLASE ALPHA-BETA PROTEIN GUANOSINE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS J.MOL.BIOL. V. 337 1149 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GMP A:1237;
B:1237;
C:1237;
D:1237;
E:1237;
F:1237;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 80 uM
283.241 C10 H13 N5 O5 c1nc2...
SO4 A:1236;
B:1236;
C:1236;
D:1236;
E:1236;
F:1236;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ODJ 2.4 Å EC: 2.4.2.28 PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS THERMUS THERMOPHILUS TRANSFERASE NUCLEOSIDE PHOSPHORYLASE ALPHA-BETA PROTEIN GUANOSINE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS J.MOL.BIOL. V. 337 1149 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ODI Kd = 62 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
2 1ODJ Kd = 80 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ODI Kd = 62 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
2 1ODJ Kd = 80 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
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 1Z35 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
2 1Z34 ic50 = 0.42 mM 2FD C10 H12 F N5 O3 c1nc2c(nc(....
3 1Z38 - NOS C10 H12 N4 O5 c1nc2c(n1[....
4 1PR1 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
5 1OUM - TAL C12 H16 N4 O4 Cc1c2c(ncn....
6 1PR2 - MDR C11 H14 N4 O3 Cc1c2c(ncn....
7 1PR5 Ki = 120 uM TBN C11 H14 N4 O4 c1cn(c2c1c....
8 1PKE - 2FD C10 H12 F N5 O3 c1nc2c(nc(....
9 1PR6 - XYA C10 H13 N5 O4 c1nc(c2c(n....
10 1PR0 - NOS C10 H12 N4 O5 c1nc2c(n1[....
11 1PK9 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
12 1OV6 - DBM C12 H16 N4 O4 Cc1c2c(ncn....
13 1PR4 - MTP C11 H14 N4 O4 S CSc1c2c(nc....
14 1PK7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
15 1OVG - MDR C11 H14 N4 O3 Cc1c2c(ncn....
16 1OU4 - 6MP C6 H6 N4 Cc1c2c(nc[....
17 1OTY - 6MP C6 H6 N4 Cc1c2c(nc[....
18 3UT6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
19 1PW7 - RAB C10 H13 N5 O4 c1nc(c2c(n....
20 1K9S - FM2 C11 H16 N5 O4 C[n+]1cnc2....
21 1A69 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
22 1VHW - ADN C10 H13 N5 O4 c1nc(c2c(n....
23 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
24 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
25 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
26 1JDV - ADN C10 H13 N5 O4 c1nc(c2c(n....
27 1JDT - MTA C11 H15 N5 O3 S CSC[C@@H]1....
28 1JE1 - GMP C10 H13 N5 O5 c1nc2c(n1[....
29 1JDZ - FMB C10 H12 N4 O5 C1=Nc2c(n[....
30 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
32 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
33 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
34 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
35 1ODI Kd = 62 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
36 1ODJ Kd = 80 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
37 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
38 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
39 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
40 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
41 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
43 4DAB - HPA C5 H4 N4 O c1[nH]c2c(....
44 3U40 - ADN C10 H13 N5 O4 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GMP; Similar ligands found: 114
No: Ligand ECFP6 Tc MDL keys Tc
1 GMP 1 1
2 5GP 0.732394 0.866667
3 G 0.732394 0.866667
4 3GP 0.704225 0.853333
5 GDP 0.684211 0.88
6 GNH 0.675325 0.868421
7 GP3 0.671053 0.857143
8 GP2 0.662338 0.846154
9 GTP 0.658228 0.88
10 2GP 0.657534 0.866667
11 GDP MG 0.64557 0.833333
12 G2P 0.641975 0.846154
13 GSP 0.641975 0.835443
14 GDP BEF 0.6375 0.8125
15 ALF 5GP 0.6375 0.802469
16 GMV 0.6375 0.857143
17 GPG 0.635294 0.87013
18 GCP 0.62963 0.857143
19 G1R 0.62963 0.868421
20 GAV 0.626506 0.846154
21 GKE 0.625 0.87013
22 GDD 0.625 0.87013
23 GDC 0.625 0.87013
24 GNP 0.621951 0.857143
25 BEF GDP 0.614458 0.802469
26 GTP MG 0.614458 0.833333
27 GCP G 0.607143 0.844156
28 GDP ALF 0.593023 0.802469
29 GDP AF3 0.593023 0.802469
30 G G 0.590909 0.844156
31 G4P 0.588235 0.866667
32 G2R 0.586207 0.846154
33 G3D 0.583333 0.866667
34 P2G 0.576923 0.815789
35 SGP 0.576923 0.78481
36 GFB 0.565217 0.846154
37 GDR 0.565217 0.846154
38 GKD 0.56383 0.87013
39 P1G 0.5625 0.805195
40 0O2 0.561798 0.866667
41 YGP 0.56044 0.792683
42 6CK 0.55914 0.825
43 G3A 0.55914 0.857143
44 Y9Z 0.554348 0.817073
45 G5P 0.553191 0.857143
46 NOS 0.549296 0.940298
47 GTG 0.548387 0.825
48 JB2 0.547368 0.846154
49 GPD 0.541667 0.814815
50 GDX 0.541667 0.857143
51 U2G 0.54 0.848101
52 GDP 7MG 0.536842 0.822785
53 C2E 0.53012 0.828947
54 PCG 0.53012 0.84
55 35G 0.53012 0.84
56 CG2 0.529412 0.848101
57 5GP 5GP 0.52381 0.815789
58 MG7 0.520548 0.957143
59 JB3 0.514852 0.835443
60 G A A A 0.504762 0.857143
61 U A G G 0.5 0.844156
62 FEG 0.495146 0.77381
63 NGD 0.495146 0.846154
64 G U34 0.490385 0.825
65 ZGP 0.490385 0.764706
66 GH3 0.488889 0.855263
67 DGP 0.487805 0.797468
68 DG 0.487805 0.797468
69 G G U 0.484848 0.820513
70 2MD 0.481132 0.785714
71 G C 0.481132 0.835443
72 BGO 0.480769 0.8125
73 GPX 0.478261 0.828947
74 XTS 0.472973 0.913043
75 DGI 0.471264 0.810127
76 CAG 0.46789 0.776471
77 MGD 0.46789 0.785714
78 I2C FE2 CMO CMO 0.463636 0.730337
79 TPG 0.45614 0.741573
80 FE9 0.455357 0.684211
81 4BW 0.454545 0.828947
82 1YD 0.454545 0.828947
83 GGM 0.453704 0.792683
84 G G G RPC 0.453704 0.7875
85 SNI 0.453333 0.898551
86 PGD 0.451327 0.814815
87 MD1 0.451327 0.785714
88 DGT 0.450549 0.810127
89 APC G U 0.45045 0.797468
90 DBG 0.443478 0.835443
91 G1R G1R 0.443478 0.835443
92 13A 0.441558 0.768293
93 GPC 0.441441 0.795181
94 PGD O 0.439655 0.75
95 DG DG 0.43299 0.802469
96 G4M 0.430894 0.797619
97 G G G C 0.429825 0.802469
98 A G C C 0.426087 0.822785
99 U G A 0.424 0.825
100 1YC 0.421569 0.802632
101 AD3 0.421053 0.882353
102 4UR 0.416667 0.828947
103 G C C C 0.411765 0.8125
104 ADN 0.410959 0.882353
105 RAB 0.410959 0.882353
106 XYA 0.410959 0.882353
107 G1G 0.408696 0.814815
108 1DA 0.407895 0.882353
109 AC2 0.407895 0.797297
110 IMP 0.406977 0.84
111 A G U 0.404762 0.825
112 3ZE 0.404494 0.772152
113 MZR 0.402778 0.838235
114 CFE 0.4 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ODJ; Ligand: GMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1odj.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1ODJ; Ligand: GMP; 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: 1odj.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1ODJ; Ligand: GMP; Similar sites found: 45
This union binding pocket(no: 3) in the query (biounit: 1odj.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4GLJ RHB 0.00004226 0.46167 1.70213
2 3LGS SAH 0.000002535 0.56904 2.55319
3 3LGS ADE 0.000002535 0.56904 2.55319
4 1IYE PGU 0.01043 0.41952 2.55319
5 3IWK NAD 0.008639 0.40867 2.55319
6 4B2Z P5S 0.02733 0.40543 2.55319
7 2WOX NDP 0.02531 0.40406 2.55319
8 3VC1 SAH 0.02392 0.41114 2.97872
9 3VC1 GST 0.02392 0.41114 2.97872
10 5MRH Q9Z 0.01139 0.40743 2.97872
11 2BII MTV 0.01247 0.40622 2.97872
12 1O9J NAD 0.02042 0.40414 2.97872
13 2A9D MTE 0.0112 0.40344 2.97872
14 5U3F 7TS 0.009377 0.40877 3.40426
15 2P4S DIH 0.00001281 0.51824 3.82979
16 1RL4 BL5 0.003161 0.46089 4.25532
17 4PZ2 NAD 0.02423 0.40169 4.25532
18 1W6P NDG GAL 0.0188 0.4026 4.47761
19 4PIO SAH 0.004912 0.43906 4.68085
20 4PIO AVI 0.004644 0.43906 4.68085
21 1YB5 NAP 0.02392 0.40528 5.10638
22 5IFK HPA 0.0000008018 0.50085 5.53191
23 1Q0S SAH 0.015 0.40392 5.53191
24 2WSB NAD 0.0324 0.40449 6.38298
25 1B8O IMH 0.000006259 0.56552 7.23404
26 5ETJ IM5 0.00002943 0.55207 7.65957
27 2A0W DIH 0.003143 0.47713 7.65957
28 4QAR ADE 0.0000007416 0.58384 9.95025
29 1G2O IMH 0.00003748 0.49598 10.2128
30 4R38 RBF 0.006678 0.41386 11.4286
31 3P0F BAU 0.00007972 0.48092 16.5957
32 1VMK GUN 0.000003135 0.48686 20.8511
33 1C3X 8IG 0.0002999 0.40344 27.6596
34 4BMX ADE 0.000006878 0.54915 28.9362
35 3BL6 FMC 0.000003717 0.56141 29.5652
36 4TXJ THM 0.000000005211 0.72173 30.2128
37 3DJF BC3 0.000006389 0.56066 31.9149
38 4WKB TDI 0.000009969 0.54689 32.3404
39 1ZOS MTM 0.000004119 0.5535 33.913
40 3KVY R2B 0.000000006012 0.59987 39.1489
41 3KVY URA 0.000008722 0.48276 39.1489
42 1NW4 IMH 0.0000000006483 0.72149 40
43 4YJK URA 0.0000005493 0.48689 40.8511
44 3EUF BAU 0.000003572 0.55311 45.1064
45 1U1F 183 0.0000001306 0.67947 47.6596
Pocket No.: 4; Query (leader) PDB : 1ODJ; Ligand: GMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1odj.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1ODJ; Ligand: GMP; 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: 1odj.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1ODJ; Ligand: GMP; 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: 1odj.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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