Receptor
PDB id Resolution Class Description Source Keywords
3GCM 2.5 Å EC: 2.7.7.8 CRYSTAL STRUCTURE OF E. COLI POLYNUCLEOTIDE PHOSPHORYLASE BOUND TO RNA AND RNASE E ESCHERICHIA COLI E24377A PROTEIN-RNA COMPLEX CYTOPLASM NUCLEOTIDYLTRANSFERASE RNA-BINDING TRANSFERASE HYDROLASE TRANSFERASE / PROTEIN BINDING COMPLEX
Ref.: CRYSTAL STRUCTURE OF ESCHERICHIA COLI POLYNUCLEOTIDE PHOSPHORYLASE CORE BOUND TO RNASE E, RNA AND MANGANESE: IMPLICATIONS FOR CATALYTIC MECHANISM AND RNA DEGRADOSOME ASSEMBLY. J.MOL.BIOL. V. 389 17 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP B:550;
B:551;
C:550;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
FLC A:550;
A:551;
B:552;
B:553;
B:554;
B:555;
C:551;
C:552;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
189.1 C6 H5 O7 C(C(=...
MG A:552;
B:556;
C:553;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GCM 2.5 Å EC: 2.7.7.8 CRYSTAL STRUCTURE OF E. COLI POLYNUCLEOTIDE PHOSPHORYLASE BOUND TO RNA AND RNASE E ESCHERICHIA COLI E24377A PROTEIN-RNA COMPLEX CYTOPLASM NUCLEOTIDYLTRANSFERASE RNA-BINDING TRANSFERASE HYDROLASE TRANSFERASE / PROTEIN BINDING COMPLEX
Ref.: CRYSTAL STRUCTURE OF ESCHERICHIA COLI POLYNUCLEOTIDE PHOSPHORYLASE CORE BOUND TO RNASE E, RNA AND MANGANESE: IMPLICATIONS FOR CATALYTIC MECHANISM AND RNA DEGRADOSOME ASSEMBLY. J.MOL.BIOL. V. 389 17 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GCM - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GCM - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3GCM - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 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 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
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 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GCM; Ligand: 5GP; 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: 3gcm.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3GCM; Ligand: 5GP; 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: 3gcm.bio1) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3GCM; Ligand: 5GP; Similar sites found: 69
This union binding pocket(no: 3) in the query (biounit: 3gcm.bio1) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GWZ SAH 0.01083 0.40391 1.35501
2 1N0U SO1 0.03642 0.40499 1.63934
3 2QRK AMP 0.01394 0.42948 1.77665
4 4R1S NAP 0.04182 0.409 1.78042
5 4NAT 2W5 0.006613 0.43726 2.5
6 4NAT ADP 0.01614 0.43726 2.5
7 2RGO FAD 0.04885 0.42247 2.55009
8 1ZEM NAD 0.007743 0.40275 2.67176
9 4C0R GDS 0.009395 0.40034 2.82258
10 1P9B IMO 0.007606 0.46805 2.94118
11 2ZKJ ADP 0.04725 0.4247 3.5533
12 3O5X JZG 0.03522 0.40166 3.62319
13 4IO2 GLU 0.0308 0.4004 3.62903
14 3O76 GTB 0.002996 0.40794 3.82775
15 5TO8 7FM 0.03784 0.4094 3.90071
16 4ZV1 ARG 0.01006 0.43337 4.29185
17 1UJ2 C5P 0.0235 0.41074 4.36508
18 3RIY NAD 0.02556 0.4295 4.3956
19 1NJR XYL 0.02533 0.44504 4.87805
20 2B9W FAD 0.004967 0.43966 4.87805
21 1GS5 NLG 0.02957 0.40173 4.87805
22 1LAF ARG 0.01198 0.41118 5.04202
23 2HNL GSH 0.00353 0.4058 6.22222
24 5EF7 5OJ 0.003744 0.40935 6.31868
25 2YVF FAD 0.007101 0.45789 7.31707
26 2YVF NAD 0.007259 0.45789 7.31707
27 3C2O NTM 0.002347 0.43725 7.31707
28 3DHV DAL AMP 0.0295 0.41238 7.31707
29 1QX4 FAD 0.01737 0.42774 8.0292
30 1G79 FMN 0.01627 0.46078 9.7561
31 1G79 PLP 0.01814 0.46078 9.7561
32 4OXI GAP 0.0151 0.43515 9.7561
33 4EBZ NAG NAG NAG NAG 0.0163 0.42351 9.7561
34 3ICT ADP 0.01594 0.41187 9.7561
35 5GS9 ARG 0.03375 0.40564 9.7561
36 5L9O GOP 0.01208 0.43302 10.0746
37 4ZSI GLP 0.00432 0.43419 10.5263
38 4ZSI 4R1 0.003423 0.43355 10.5263
39 1QF5 GDP 0.003434 0.47514 12.1951
40 3N26 ARG 0.002034 0.45676 12.1951
41 3R5J ACE ALA ASP VAL ALA ASA 0.02312 0.40985 12.1951
42 4MSG 2C6 0.02212 0.40587 12.1951
43 3K00 MTT 0.01768 0.40323 12.1951
44 5DX1 SFG 0.01108 0.40216 12.1951
45 3K37 BCZ 0.02756 0.45181 14.6341
46 5LIA 6XN 0.01623 0.44595 14.6341
47 2CIG 1DG 0.01971 0.42794 14.6341
48 1U9Q 186 0.03104 0.41404 14.6341
49 5ECP JAA 0.03874 0.41279 14.6341
50 5ECP MET 0.03874 0.41279 14.6341
51 5ECP ATP 0.03993 0.41279 14.6341
52 3RG9 NDP 0.01713 0.40718 14.6341
53 3RG9 WRA 0.01897 0.40718 14.6341
54 3U3Z SEP GLN GLU PTR 0.04176 0.40652 14.6341
55 1I1D COA 0.02008 0.40076 16.7702
56 3RZ3 U94 0.008977 0.44992 17.0732
57 4PVV HO4 0.04184 0.44015 17.0732
58 5D9X GSH 0.01161 0.42631 17.0732
59 3NWQ 2NC 0.02971 0.40125 18.1818
60 5I34 IMP 0.007644 0.44741 19.5122
61 4X7G 3Y8 0.006705 0.41492 19.5122
62 2Y7I ARG 0.003548 0.4311 21.9512
63 1AMU AMP 0.01817 0.42739 21.9512
64 1VB3 KPA 0.003765 0.45273 24.3902
65 4JBI NDP 0.04905 0.41814 24.3902
66 5G3U ITW 0.04313 0.41761 29.2683
67 5G3U FDA 0.04431 0.40944 29.2683
68 3T3C 017 0.006836 0.44572 37.3737
69 4USR FAD 0.02597 0.41422 39.0244
Feedback