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Receptor
PDB id Resolution Class Description Source Keywords
1IYB 1.5 Å EC: 3.1.-.- CRYSTAL STRUCTURE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NW NICOTIANA GLUTINOSA HYDROLASE RIBONUCLEASE
Ref.: GUANINE BINDING SITE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NW REVEALED BY X-RAY CRYSTALLOGRAPHY BIOCHEMISTRY V. 41 15195 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:1295;
B:1296;
Valid;
Valid;
none;
none;
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363.221 C10 H14 N5 O8 P c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1IYB 1.5 Å EC: 3.1.-.- CRYSTAL STRUCTURE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NW NICOTIANA GLUTINOSA HYDROLASE RIBONUCLEASE
Ref.: GUANINE BINDING SITE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NW REVEALED BY X-RAY CRYSTALLOGRAPHY BIOCHEMISTRY V. 41 15195 2002
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1VD1 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 1VCZ - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
4 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UCA - U2P C9 H13 N2 O9 P C1=CN(C(=O....
2 1V9H - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 1UCC - U3P C9 H13 N2 O9 P C1=CN(C(=O....
4 1J1F - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
5 1UCD - URA C4 H4 N2 O2 C1=CNC(=O)....
6 1J1G - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
7 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; 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 G1R 0.765432 0.973333
11 GCP 0.765432 0.960526
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 GMP 0.732394 0.866667
18 GPG 0.724138 0.948052
19 G2R 0.712644 0.948052
20 ALF GDP 0.701149 0.9
21 GDP ALF 0.701149 0.9
22 GDP AF3 0.701149 0.9
23 GKE 0.692308 0.948052
24 Y9Z 0.692308 0.890244
25 GDC 0.692308 0.948052
26 GDD 0.692308 0.948052
27 YGP 0.681319 0.9125
28 G3A 0.677419 0.960526
29 G5P 0.670213 0.960526
30 GFB 0.666667 0.948052
31 GDR 0.666667 0.948052
32 GTG 0.666667 0.924051
33 6CK 0.659574 0.924051
34 3GP 0.65 0.959459
35 G G 0.648936 0.960526
36 GKD 0.645833 0.948052
37 JB2 0.645833 0.948052
38 GDX 0.639175 0.960526
39 GPD 0.639175 0.9125
40 GDP 7MG 0.635417 0.923077
41 G3D 0.617977 0.972973
42 U2G 0.617647 0.924051
43 2GP 0.609756 0.946667
44 IMP 0.609756 0.972603
45 JB3 0.607843 0.935897
46 CG2 0.605769 0.924051
47 G4P 0.604396 0.972973
48 DGP 0.60241 0.922078
49 DG 0.60241 0.922078
50 FEG 0.601942 0.890244
51 NGD 0.601942 0.948052
52 ZGP 0.596154 0.879518
53 0O2 0.595745 0.972973
54 2MD 0.584906 0.879518
55 G7M 0.583333 0.960526
56 CAG 0.583333 0.869048
57 G A A A 0.579439 0.935065
58 A G 0.579439 0.947368
59 U A G G 0.574074 0.947368
60 MGD 0.568807 0.879518
61 DBG 0.566372 0.935897
62 PGD 0.5625 0.9125
63 MD1 0.5625 0.879518
64 P2G 0.55814 0.894737
65 GCP G 0.556701 0.933333
66 FE9 0.553571 0.784946
67 P1G 0.545455 0.883117
68 GH3 0.542553 0.96
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 G U 0.522936 0.911392
74 PGD O 0.521368 0.83908
75 DGT 0.521277 0.910256
76 G4M 0.520325 0.869048
77 AKW 0.513761 0.878049
78 G C 0.513514 0.911392
79 93A 0.511364 0.821429
80 IDP 0.505495 0.959459
81 MGQ 0.505155 0.948052
82 C2R 0.5 0.893333
83 A 0.5 0.905405
84 AMZ 0.5 0.905405
85 BGO 0.5 0.911392
86 AMP 0.5 0.905405
87 AIR 0.493671 0.890411
88 MGV 0.49 0.901235
89 SGP 0.488889 0.8375
90 NIA 0.488095 0.8375
91 GPC 0.474138 0.890244
92 G G G RPC 0.473684 0.886076
93 GGM 0.473684 0.888889
94 71V 0.47191 0.85
95 APC G U 0.470085 0.897436
96 R5I 0.46875 0.933333
97 R7I 0.46875 0.933333
98 MGP 0.46875 0.948052
99 35G 0.468085 0.945946
100 PCG 0.468085 0.945946
101 C2E 0.468085 0.933333
102 G1G 0.466102 0.9125
103 AAM 0.465909 0.905405
104 RMB 0.465909 0.813333
105 FAI 0.465909 0.905405
106 7RA 0.465909 0.918919
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 JLN 0.433333 0.88
124 P2P 0.433333 0.842105
125 A G U U 0.42963 0.9
126 XMP 0.428571 0.907895
127 PGS 0.425532 0.804878
128 RVP 0.423529 0.84
129 G2Q 0.423077 0.948052
130 ADP 0.419355 0.906667
131 ABM 0.417582 0.857143
132 A2D 0.417582 0.881579
133 PRT 0.416667 0.945946
134 GUO 0.415842 0.932432
135 AT4 0.414894 0.871795
136 CA0 0.410526 0.883117
137 2SA 0.41 0.871795
138 1YD 0.409091 0.933333
139 4BW 0.409091 0.933333
140 A12 0.408602 0.871795
141 AP2 0.408602 0.871795
142 BA3 0.408602 0.881579
143 6C6 0.408163 0.825
144 25A 0.407767 0.906667
145 NOS 0.406977 0.813333
146 HEJ 0.40625 0.906667
147 ATP 0.40625 0.906667
148 AP5 0.404255 0.881579
149 B4P 0.404255 0.881579
150 ACQ 0.40404 0.883117
151 6IA 0.40404 0.785714
152 ANP 0.40404 0.883117
153 CGP 0.403361 0.878049
154 APC 0.402062 0.871795
155 3ZE 0.402062 0.871795
156 5FA 0.402062 0.906667
157 AQP 0.402062 0.906667
158 N6P 0.4 0.853333
159 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1IYB; Ligand: 5GP; Similar sites found with APoc: 80
This union binding pocket(no: 1) in the query (biounit: 1iyb.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1PZO CBT None
2 3KP6 SAL None
3 1DCP HBI None
4 3A06 FOM 0.961538
5 1DKU AP2 1.44231
6 3QMK SGN IDS SGN IDS 1.44231
7 1XAP TTB 1.44231
8 1SQS TLA 1.44231
9 2BYC FMN 1.45985
10 3FC2 IBI 1.49254
11 5D9J 0N8 2.13904
12 3OND ADN 2.40385
13 3OND NAD 2.40385
14 3IQE F42 2.40385
15 3DLA NXX 2.40385
16 4YBN FAD 2.67857
17 4OYA 1VE 2.88462
18 6FHO FAD 2.88462
19 2JLD AG1 2.88462
20 2QA1 FAD 2.88462
21 2PUL ACP 3.84615
22 2QZS 250 3.84615
23 2QZS GLC 3.84615
24 2QZS ADP 3.84615
25 1FC4 AKB PLP 3.84615
26 1MUU NAD 3.84615
27 5G3U FDA 4.32692
28 5UWA 8ND 4.32692
29 1KGZ PRP 4.32692
30 4U0W 16G 4.32692
31 3QKD HI0 4.97238
32 1TV5 N8E 5.28846
33 4UP4 GAL NAG 5.28846
34 3FAP ARD 5.31915
35 5GPG RAP 5.37634
36 3AKK ADP 5.76923
37 5L92 C0R 5.76923
38 1DJN ADP 5.76923
39 1JQ9 PHE LEU SER TYR LYS 5.78512
40 1MAI I3P 6.10687
41 3WDM ADN 6.73077
42 5UCD NAP 7.21154
43 6F7L FAD 7.69231
44 5G3N X28 7.87402
45 5M67 3D1 8.65385
46 5M67 ADE 8.65385
47 5M67 NAD 8.65385
48 4QWT ACD 8.65385
49 5ZZ6 NAD 8.65385
50 4FAJ LEU VAL THR LEU VAL PHE VAL 8.65385
51 5B2E MQG 8.65385
52 1U1B PAX 8.87097
53 2ZJ1 NAD 9.13461
54 2ZJ1 ARJ 9.13461
55 1H8P PC 9.17431
56 5J6H NCA 9.61539
57 4X7R NTO 9.61539
58 4X7R 3YW 9.61539
59 4X7R UDP 9.61539
60 6F3M NAD 10.0962
61 1AUX AGS 10.0962
62 1PK8 ATP 10.0962
63 3NJ4 NAD 10.5769
64 1FP1 HCC 11.5385
65 5JE8 NAD 12.0192
66 5V4R MGT 13.4615
67 1YNH SUO 13.4615
68 4D9C PMP 13.4615
69 5MWY YNU 13.9423
70 2ZE3 AKG 14.9038
71 4DW4 U5P 16.1677
72 4YSX FAD 16.8269
73 2F5Z FAD 17.1875
74 2EA1 GPG 21.6346
75 5ZCO CHD 23.4043
76 2DYS PGV 23.4043
77 2DYR PGV 23.4043
78 5ZCO PGV 23.4043
79 5Z84 PGV 23.4043
80 5Z84 CHD 23.4043
Pocket No.: 2; Query (leader) PDB : 1IYB; Ligand: 5GP; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 1iyb.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1X0P FAD None
2 5TA6 79D 1.39665
3 2HFN FMN 1.96078
4 1I7L ATP 2.88462
5 3VPD ANP 3.36538
6 1ECE BGC BGC BGC BGC 3.36538
7 1NF8 BOG 3.38164
8 1BGQ RDC 3.84615
9 4I6H 1C8 4.32692
10 4ZBR DIF 5.76923
11 5VZ0 ADP 6.25
12 6F68 GSH 6.73077
13 6F68 4EU 6.73077
14 5J5R 6G1 9.51157
15 5J5R IMP 9.51157
16 5IKH 6BW 9.61539
17 5ZCT ANP 10.0962
18 2VPY MGD 10.2564
19 3VPB ADP 10.5769
20 5K2M ADP 30.1887
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