Receptor
PDB id Resolution Class Description Source Keywords
4NKU 1.94 Å EC: 2.7.7.- STRUCTURE OF CID1 IN COMPLEX WITH ITS SHORT PRODUCT APU SCHIZOSACCHAROMYCES POMBE POLY(U) POLYMERASE NUCLEOTIDYL TRANFER DOMAIN PAP-ASSOCIATDOMAIN UTP BINDING TRANSFERASE-RNA COMPLEX
Ref.: A CRITICAL SWITCH IN THE ENZYMATIC PROPERTIES OF TH PROTEIN DECIPHERED FROM ITS PRODUCT-BOUND CRYSTAL S NUCLEIC ACIDS RES. V. 42 3372 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A U D:58;
H:58;
Valid;
Valid;
none;
none;
submit data
572.404 n/a P(=O)...
BR D:101;
B:402;
A:403;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
79.904 Br [Br-]
MG A:401;
A:402;
B:401;
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
4NKT 1.9 Å EC: 2.7.7.- STRUCTURE OF CID1 IN COMPLEX WITH THE UTP ANALOG UMPNPP SCHIZOSACCHAROMYCES POMBE POLY(U) POLYMERASE NUCLEOTIDYL TRANFER DOMAIN PAP-ASSOCIATDOMAIN UTP BINDING TRANSFERASE
Ref.: A CRITICAL SWITCH IN THE ENZYMATIC PROPERTIES OF TH PROTEIN DECIPHERED FROM ITS PRODUCT-BOUND CRYSTAL S NUCLEIC ACIDS RES. V. 42 3372 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 4FHW - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4NKU - A U n/a n/a
3 4NKT - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
4 4FH5 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
5 4FHV - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
6 4EP7 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
7 4FHP - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 4FHW - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4NKU - A U n/a n/a
3 4NKT - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
4 4FH5 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
5 4FHV - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
6 4EP7 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
7 4FHP - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 4FHW - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4NKU - A U n/a n/a
3 4NKT - 2KH C9 H16 N3 O14 P3 C1=CN(C(=O....
4 4FH5 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
5 4FHV - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
6 4EP7 - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
7 4FHP - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A U ; Similar ligands found: 193
No: Ligand ECFP6 Tc MDL keys Tc
1 A U 1 1
2 A U C C 0.813559 0.973684
3 U A A U 0.801724 0.960526
4 A G U 0.801653 0.936709
5 A G U U 0.769841 0.936709
6 U A 0.741379 0.960526
7 A C A C 0.697479 0.973684
8 UP5 0.690265 0.947368
9 G U 0.689655 0.924051
10 4TC 0.678261 0.923077
11 APU 0.672414 0.947368
12 U A C C 0.642276 0.960526
13 UPA 0.608333 0.960526
14 A A 0.584071 0.894737
15 G A A A 0.579365 0.898734
16 PUA 0.557252 0.8875
17 ATP A A A 0.550847 0.932432
18 ATP A 0.550847 0.932432
19 G C 0.546875 0.924051
20 U U 0.544643 0.842105
21 139 0.543307 0.924051
22 A G 0.542636 0.886076
23 U A G G 0.538462 0.886076
24 A A A 0.534483 0.883117
25 UDP UDP 0.524272 0.851351
26 3AM 0.519608 0.855263
27 ADP MG 0.509259 0.918919
28 SFB 0.507812 0.777778
29 A3P 0.504673 0.868421
30 APC G U 0.496296 0.839506
31 U5P 0.49505 0.815789
32 U 0.49505 0.815789
33 PAP 0.491071 0.857143
34 UPU 0.486486 0.853333
35 PAX 0.485714 0.878049
36 G U34 0.484848 0.9125
37 ADP BMA 0.483333 0.921053
38 UDP 0.481132 0.805195
39 ATP MG 0.477876 0.918919
40 ADP PO3 0.477876 0.918919
41 A 0.471698 0.868421
42 AMP 0.471698 0.868421
43 CSQ 0.471545 0.825
44 CSV 0.471545 0.825
45 VO4 ADP 0.470085 0.883117
46 ADP VO4 0.470085 0.883117
47 GAP 0.469565 0.921053
48 G G G C 0.467626 0.9125
49 44P 0.466667 0.775
50 PPS 0.465517 0.767442
51 A G C C 0.464286 0.911392
52 A12 0.463636 0.8375
53 AP2 0.463636 0.8375
54 4TA 0.463235 0.901235
55 0WD 0.463235 0.898734
56 ALF ADP 0.461538 0.85
57 UPG 0.461538 0.831169
58 UFM 0.461538 0.831169
59 ADP ALF 0.461538 0.85
60 GDU 0.461538 0.831169
61 GUD 0.461538 0.831169
62 ADP 0.459459 0.87013
63 PO4 PO4 A A A A PO4 0.459016 0.905405
64 UTP 0.454545 0.805195
65 U U U U 0.452991 0.828947
66 APC MG 0.452174 0.894737
67 G C C C 0.451389 0.9
68 U5F 0.45045 0.805195
69 UPF 0.45 0.790123
70 U2F 0.45 0.790123
71 DAL AMP 0.45 0.907895
72 URM 0.449153 0.820513
73 660 0.449153 0.820513
74 LQJ 0.448819 0.894737
75 MYR AMP 0.448 0.821429
76 ACP 0.447368 0.848101
77 A2D 0.445455 0.894737
78 ABM 0.445455 0.846154
79 45A 0.445455 0.846154
80 Y6W 0.445378 0.790123
81 Z5A 0.444444 0.869048
82 APC 0.443478 0.8375
83 PRX 0.443478 0.825
84 NAJ PZO 0.442857 0.923077
85 ADQ 0.442623 0.896104
86 AN2 0.442478 0.858974
87 C C C C 0.441667 0.881579
88 SRA 0.440367 0.825
89 SAP 0.439655 0.82716
90 AGS 0.439655 0.82716
91 A22 0.438017 0.883117
92 UFG 0.438017 0.790123
93 2KH 0.4375 0.78481
94 A2P 0.4375 0.855263
95 BA3 0.4375 0.894737
96 UTP U U U 0.436975 0.837838
97 3UC 0.435484 0.790123
98 ATP 0.434783 0.87013
99 HEJ 0.434783 0.87013
100 25A 0.434426 0.894737
101 TYR AMP 0.434109 0.897436
102 AMP DBH 0.434109 0.871795
103 AP5 0.433628 0.894737
104 B4P 0.433628 0.894737
105 5AS 0.433628 0.744444
106 T99 0.432203 0.8375
107 TAT 0.432203 0.8375
108 ACQ 0.432203 0.848101
109 NMN AMP PO4 0.431655 0.947368
110 5FA 0.431034 0.87013
111 AQP 0.431034 0.87013
112 AT4 0.429825 0.8375
113 UNP 0.429825 0.78481
114 HQG 0.429752 0.858974
115 UDH 0.428571 0.771084
116 AR6 AR6 0.427481 0.92
117 RBY 0.42735 0.8375
118 ADV 0.42735 0.8375
119 ATR 0.42735 0.844156
120 M33 0.426087 0.858974
121 ADX 0.426087 0.788235
122 CA0 0.426087 0.871795
123 AU1 0.426087 0.848101
124 DU DU DU DU BRU DA DU 0.425806 0.86747
125 UDM 0.425197 0.810127
126 ATF 0.425 0.8375
127 9BG 0.42446 0.851852
128 URI 0.424242 0.76
129 KG4 0.422414 0.871795
130 50T 0.422414 0.835443
131 TXE 0.422222 0.910256
132 6YZ 0.421488 0.848101
133 NAJ PYZ 0.42069 0.878049
134 T5A 0.42029 0.86747
135 ANP 0.420168 0.848101
136 USQ 0.419355 0.715909
137 4AD 0.419355 0.873418
138 AR6 0.418803 0.87013
139 APR 0.418803 0.87013
140 UD1 0.418605 0.820513
141 UD2 0.418605 0.820513
142 LMS 0.418182 0.767442
143 SON 0.417391 0.860759
144 8LE 0.416667 0.85
145 C C 0.416667 0.868421
146 ARG AMP 0.416667 0.833333
147 7D5 0.416667 0.810127
148 UPP 0.416667 0.831169
149 G3N 0.416 0.810127
150 AD9 0.415254 0.848101
151 U3P 0.415094 0.802632
152 UA3 0.415094 0.802632
153 6V0 0.414815 0.898734
154 NAI 0.414815 0.910256
155 NAX 0.414815 0.876543
156 UDX 0.414634 0.807692
157 UAD 0.414634 0.807692
158 8LQ 0.414634 0.860759
159 25L 0.414062 0.883117
160 AV2 0.413223 0.8
161 U2G 0.413043 0.888889
162 2AM 0.412844 0.844156
163 9X8 0.412698 0.82716
164 4UV 0.412214 0.897436
165 ADN 0.411765 0.8
166 RAB 0.411765 0.8
167 XYA 0.411765 0.8
168 AF3 ADP 3PG 0.411765 0.841463
169 5SV 0.41129 0.785714
170 8LH 0.409836 0.884615
171 G3A 0.409091 0.851852
172 AP0 0.408759 0.875
173 A3R 0.408 0.839506
174 LPA AMP 0.407407 0.821429
175 2A5 0.40678 0.825
176 A2R 0.406504 0.858974
177 1ZZ 0.40625 0.8
178 G5P 0.406015 0.851852
179 4UU 0.406015 0.897436
180 5AL 0.404959 0.883117
181 TXD 0.404412 0.886076
182 G G G RPC 0.404255 0.898734
183 UDP ALA FGA CYS DAL DAL MUB C C A9Z 0.403587 0.795699
184 7D3 0.403509 0.8125
185 MAP 0.403226 0.82716
186 G G 0.401515 0.875
187 P1H 0.401316 0.855422
188 OOB 0.4 0.907895
189 NPW 0.4 0.865854
190 OZV 0.4 0.87013
191 9SN 0.4 0.851852
192 NDP 0.4 0.898734
193 AHZ 0.4 0.821429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NKT; Ligand: 2KH; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 4nkt.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3HIY UTP 19.6481
2 3HIY UTP 19.6481
3 3HJ1 UTP 38.1232
4 2Q0D ATP 38.8102
5 5W0N 2KH 49.2669
6 5W0N 2KH 49.2669
7 5W0N 2KH 49.2669
Pocket No.: 2; Query (leader) PDB : 4NKT; Ligand: 2KH; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 4nkt.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3HJ1 UTP 38.1232
2 2Q0D ATP 38.8102
3 5W0N 2KH 49.2669
4 5W0N 2KH 49.2669
5 5W0N 2KH 49.2669
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