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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: 179
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 G C 0.546875 0.924051
19 U U 0.544643 0.842105
20 139 0.543307 0.924051
21 A G 0.542636 0.886076
22 U A G G 0.538462 0.886076
23 A A A 0.534483 0.883117
24 UDP UDP 0.524272 0.851351
25 3AM 0.519608 0.855263
26 SFB 0.507812 0.777778
27 A3P 0.504673 0.868421
28 APC G U 0.496296 0.839506
29 U 0.49505 0.815789
30 U5P 0.49505 0.815789
31 PAP 0.491071 0.857143
32 UPU 0.486486 0.853333
33 PAX 0.485714 0.878049
34 G U34 0.484848 0.9125
35 ADP BMA 0.483333 0.921053
36 UDP 0.481132 0.805195
37 ADP PO3 0.477876 0.918919
38 AMP 0.471698 0.868421
39 A 0.471698 0.868421
40 CSV 0.471545 0.825
41 CSQ 0.471545 0.825
42 ADP VO4 0.470085 0.883117
43 VO4 ADP 0.470085 0.883117
44 GAP 0.469565 0.921053
45 G G G C 0.467626 0.9125
46 44P 0.466667 0.775
47 PPS 0.465517 0.767442
48 A G C C 0.464286 0.911392
49 A12 0.463636 0.8375
50 AP2 0.463636 0.8375
51 4TA 0.463235 0.901235
52 0WD 0.463235 0.898734
53 ADP ALF 0.461538 0.85
54 UPG 0.461538 0.831169
55 GDU 0.461538 0.831169
56 GUD 0.461538 0.831169
57 ALF ADP 0.461538 0.85
58 UFM 0.461538 0.831169
59 ADP 0.459459 0.87013
60 PO4 PO4 A A A A PO4 0.459016 0.905405
61 UTP 0.454545 0.805195
62 U U U U 0.452991 0.828947
63 G C C C 0.451389 0.9
64 U2F 0.45 0.790123
65 UPF 0.45 0.790123
66 DAL AMP 0.45 0.907895
67 URM 0.449153 0.820513
68 660 0.449153 0.820513
69 MYR AMP 0.448 0.821429
70 ACP 0.447368 0.848101
71 A2D 0.445455 0.894737
72 ABM 0.445455 0.846154
73 Y6W 0.445378 0.790123
74 Z5A 0.444444 0.869048
75 PRX 0.443478 0.825
76 APC 0.443478 0.8375
77 NAJ PZO 0.442857 0.923077
78 ADQ 0.442623 0.896104
79 AN2 0.442478 0.858974
80 C C C C 0.441667 0.881579
81 SRA 0.440367 0.825
82 SAP 0.439655 0.82716
83 AGS 0.439655 0.82716
84 A22 0.438017 0.883117
85 UFG 0.438017 0.790123
86 2KH 0.4375 0.78481
87 BA3 0.4375 0.894737
88 A2P 0.4375 0.855263
89 UTP U U U 0.436975 0.837838
90 3UC 0.435484 0.790123
91 HEJ 0.434783 0.87013
92 ATP 0.434783 0.87013
93 25A 0.434426 0.894737
94 AMP DBH 0.434109 0.871795
95 TYR AMP 0.434109 0.897436
96 AP5 0.433628 0.894737
97 B4P 0.433628 0.894737
98 5AS 0.433628 0.744444
99 ACQ 0.432203 0.848101
100 TAT 0.432203 0.8375
101 T99 0.432203 0.8375
102 NMN AMP PO4 0.431655 0.947368
103 5FA 0.431034 0.87013
104 AQP 0.431034 0.87013
105 AT4 0.429825 0.8375
106 UNP 0.429825 0.78481
107 UDH 0.428571 0.771084
108 AR6 AR6 0.427481 0.92
109 ADV 0.42735 0.8375
110 ATR 0.42735 0.844156
111 RBY 0.42735 0.8375
112 ADX 0.426087 0.788235
113 AU1 0.426087 0.848101
114 CA0 0.426087 0.871795
115 M33 0.426087 0.858974
116 DU DU DU DU BRU DA DU 0.425806 0.86747
117 UDM 0.425197 0.810127
118 ATF 0.425 0.8375
119 URI 0.424242 0.76
120 50T 0.422414 0.835443
121 TXE 0.422222 0.910256
122 6YZ 0.421488 0.848101
123 NAJ PYZ 0.42069 0.878049
124 T5A 0.42029 0.86747
125 ANP 0.420168 0.848101
126 USQ 0.419355 0.715909
127 4AD 0.419355 0.873418
128 AR6 0.418803 0.87013
129 APR 0.418803 0.87013
130 UD1 0.418605 0.820513
131 UD2 0.418605 0.820513
132 LMS 0.418182 0.767442
133 SON 0.417391 0.860759
134 7D5 0.416667 0.810127
135 UPP 0.416667 0.831169
136 C C 0.416667 0.868421
137 ARG AMP 0.416667 0.833333
138 G3N 0.416 0.810127
139 AD9 0.415254 0.848101
140 UA3 0.415094 0.802632
141 U3P 0.415094 0.802632
142 6V0 0.414815 0.898734
143 NAX 0.414815 0.876543
144 NAI 0.414815 0.910256
145 UAD 0.414634 0.807692
146 UDX 0.414634 0.807692
147 25L 0.414062 0.883117
148 AV2 0.413223 0.8
149 U2G 0.413043 0.888889
150 2AM 0.412844 0.844156
151 9X8 0.412698 0.82716
152 4UV 0.412214 0.897436
153 XYA 0.411765 0.8
154 AF3 ADP 3PG 0.411765 0.841463
155 ADN 0.411765 0.8
156 RAB 0.411765 0.8
157 5SV 0.41129 0.785714
158 G3A 0.409091 0.851852
159 AP0 0.408759 0.875
160 A3R 0.408 0.839506
161 LPA AMP 0.407407 0.821429
162 2A5 0.40678 0.825
163 A2R 0.406504 0.858974
164 1ZZ 0.40625 0.8
165 4UU 0.406015 0.897436
166 G5P 0.406015 0.851852
167 5AL 0.404959 0.883117
168 TXD 0.404412 0.886076
169 G G G RPC 0.404255 0.898734
170 UDP ALA FGA CYS DAL DAL MUB C C A9Z 0.403587 0.795699
171 7D3 0.403509 0.8125
172 MAP 0.403226 0.82716
173 G G 0.401515 0.875
174 P1H 0.401316 0.855422
175 NDP 0.4 0.898734
176 OOB 0.4 0.907895
177 9SN 0.4 0.851852
178 NPW 0.4 0.865854
179 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: 56
This union binding pocket(no: 1) in the query (biounit: 4nkt.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5TVI MYR None
2 1RV1 IMZ None
3 3O01 DXC 1.2987
4 1RYI FAD 2.05279
5 1RYI GOA 2.05279
6 1ZED PNP 2.05279
7 4XJ6 GH3 2.93255
8 3ER9 3AT 3.0303
9 2YIV YIV 3.22581
10 5OC1 FAD 3.22581
11 3GDN HBX 3.22581
12 3GDN FAD 3.22581
13 4HA6 FAD 3.51906
14 1LVK MNT BEF 3.51906
15 2GWH PCI 3.69128
16 3KRU FMN 3.81232
17 6MVU K4V 3.81232
18 4UP4 GAL NAG 4.10557
19 4HZ0 1AV 4.22535
20 1JGS SAL 4.34783
21 2HHP FLC 4.39883
22 1GJW GLC 4.39883
23 5LPA 71R 4.44444
24 5LPA ATP 4.44444
25 3GD8 GOL 4.4843
26 3KP6 SAL 4.63576
27 4TQK NAG 4.69208
28 3JYY PPV 4.87805
29 6EBQ FMN 5
30 5EB4 FAD 5.27859
31 6H5E ANP 5.57769
32 5NM7 GLY 5.6391
33 1W3T 3GR 6.12245
34 6CB2 OLC 6.14334
35 1DTL BEP 6.21118
36 1R89 CTP 6.86499
37 4U03 TLL 7.03812
38 4U03 GTP 7.03812
39 3QVP FAD 7.62463
40 2D5X L35 8.21918
41 3JZ0 APC 8.36237
42 1NAA 6FA 8.79765
43 1Q79 3AT 9.38416
44 4JLZ UTP 10.5572
45 4O4Z N2O 12.3377
46 3N7S 3N7 13.913
47 5N26 CPT 17.033
48 1UO5 PIH 17.6471
49 3HIY UTP 19.6481
50 2B56 UTP 25.5132
51 2B56 U5P 25.5132
52 5I49 2KH 28.739
53 5A2Z GTP 36.9501
54 3HJ1 UTP 38.1232
55 2Q0D ATP 38.8102
56 5W0N 2KH 49.2669
Pocket No.: 2; Query (leader) PDB : 4NKT; Ligand: 2KH; Similar sites found with APoc: 24
This union binding pocket(no: 2) in the query (biounit: 4nkt.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 6BKL RIM None
2 4WG0 CHD None
3 6BKL EU7 None
4 3RV5 DXC 2.24719
5 2P3V SRT 2.73438
6 3CH6 NAP 2.7972
7 3CH6 311 2.7972
8 4RM0 FUC NAG GAL 3.48101
9 4OAG ADP 3.58209
10 4ICS TRP GLY 3.81232
11 2GL0 ADN 4.19162
12 3ACT BGC 4.39883
13 4OAV PUP 4.69208
14 2JFV FLC 4.811
15 4BC5 5FX 4.98534
16 3DTU DXC 5.34351
17 4X7Y SAH 6.93431
18 5CX6 CDP 7.03812
19 1MT1 AG2 9.61539
20 1N13 AG2 9.61539
21 5Z84 CHD 10.2041
22 5ZCO CHD 10.2041
23 5OCA 9QZ 13.0252
24 1UO4 PIH 17.6471
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