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+](...
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 18 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 17 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 17 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: 176
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 UP5 0.690265 0.947368
6 4TC 0.678261 0.923077
7 APU 0.672414 0.947368
8 U G A 0.671756 0.936709
9 U A C C 0.642276 0.960526
10 UPA 0.608333 0.960526
11 A A 0.584071 0.894737
12 G A A A 0.579365 0.898734
13 PUA 0.557252 0.8875
14 ATP A A A 0.550847 0.932432
15 G C 0.546875 0.924051
16 U U 0.544643 0.842105
17 139 0.543307 0.924051
18 U A G G 0.538462 0.886076
19 A A A 0.534483 0.883117
20 UDP UDP 0.524272 0.851351
21 3AM 0.519608 0.855263
22 BEF ADP 0.513761 0.860759
23 ADP BEF 0.513761 0.860759
24 UDP GAL 0.513043 0.855263
25 SFB 0.507812 0.777778
26 A3P 0.504673 0.868421
27 ADP MG 0.504587 0.883117
28 APC G U 0.496296 0.839506
29 U5P 0.49505 0.815789
30 PAP 0.491071 0.857143
31 UPU 0.486486 0.853333
32 PAX 0.485714 0.878049
33 G U34 0.484848 0.9125
34 ADP BMA 0.483333 0.921053
35 ANP MG 0.482759 0.85
36 UDP 0.481132 0.805195
37 ADP PO3 0.477876 0.918919
38 AMP MG 0.476636 0.87013
39 ATP MG 0.473684 0.883117
40 A 0.471698 0.868421
41 AMP 0.471698 0.868421
42 CSV 0.471545 0.825
43 CSQ 0.471545 0.825
44 ADP VO4 0.470085 0.883117
45 VO4 ADP 0.470085 0.883117
46 GAP 0.469565 0.921053
47 G G G C 0.467626 0.9125
48 OMC OMU OMG OMG U 0.466667 0.890244
49 44P 0.466667 0.775
50 PPS 0.465517 0.767442
51 A G C C 0.464286 0.911392
52 AP2 0.463636 0.8375
53 A12 0.463636 0.8375
54 4TA 0.463235 0.901235
55 0WD 0.463235 0.898734
56 UFM 0.461538 0.831169
57 UPG 0.461538 0.831169
58 ADP ALF 0.461538 0.85
59 GUD 0.461538 0.831169
60 ALF ADP 0.461538 0.85
61 GDU 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 G C C C 0.451389 0.9
67 UPF 0.45 0.790123
68 U2F 0.45 0.790123
69 DAL AMP 0.45 0.907895
70 660 0.449153 0.820513
71 URM 0.449153 0.820513
72 MYR AMP 0.448 0.821429
73 ACP 0.447368 0.848101
74 ABM 0.445455 0.846154
75 A2D 0.445455 0.894737
76 Y6W 0.445378 0.790123
77 Z5A 0.444444 0.869048
78 PRX 0.443478 0.825
79 APC 0.443478 0.8375
80 DU DU DU DU BRU DA DU 0.442953 0.86747
81 NAJ PZO 0.442857 0.923077
82 ADQ 0.442623 0.896104
83 AN2 0.442478 0.858974
84 SRA 0.440367 0.825
85 SAP 0.439655 0.82716
86 AGS 0.439655 0.82716
87 A22 0.438017 0.883117
88 UFG 0.438017 0.790123
89 BA3 0.4375 0.894737
90 A2P 0.4375 0.855263
91 2KH 0.4375 0.78481
92 UTP U U U 0.436975 0.837838
93 3UC 0.435484 0.790123
94 ATP 0.434783 0.87013
95 25A 0.434426 0.894737
96 AMP DBH 0.434109 0.871795
97 5AS 0.433628 0.744444
98 AP5 0.433628 0.894737
99 B4P 0.433628 0.894737
100 TAT 0.432203 0.8375
101 ACQ 0.432203 0.848101
102 NMN AMP PO4 0.431655 0.947368
103 AQP 0.431034 0.87013
104 5FA 0.431034 0.87013
105 UNP 0.429825 0.78481
106 UDH 0.428571 0.771084
107 AR6 AR6 0.427481 0.92
108 ATR 0.42735 0.844156
109 ADV 0.42735 0.8375
110 RBY 0.42735 0.8375
111 TYR AMP 0.426357 0.909091
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 UDM 0.425197 0.810127
117 ATF 0.425 0.8375
118 URI 0.424242 0.76
119 U 0.424242 0.76
120 50T 0.422414 0.835443
121 TXE 0.422222 0.910256
122 T5A 0.42029 0.86747
123 ANP 0.420168 0.848101
124 USQ 0.419355 0.715909
125 4AD 0.419355 0.873418
126 APR 0.418803 0.87013
127 AR6 0.418803 0.87013
128 UD1 0.418605 0.820513
129 UD2 0.418605 0.820513
130 SON 0.417391 0.860759
131 7D5 0.416667 0.810127
132 UPP 0.416667 0.831169
133 C C 0.416667 0.868421
134 G3N 0.416 0.810127
135 AD9 0.415254 0.848101
136 U3P 0.415094 0.802632
137 UA3 0.415094 0.802632
138 NAI 0.414815 0.910256
139 6V0 0.414815 0.898734
140 NAX 0.414815 0.876543
141 UAD 0.414634 0.807692
142 UDX 0.414634 0.807692
143 25L 0.414062 0.883117
144 AV2 0.413223 0.8
145 U2G 0.413043 0.888889
146 2AM 0.412844 0.844156
147 4UV 0.412214 0.897436
148 AF3 ADP 3PG 0.411765 0.841463
149 ADN 0.411765 0.8
150 RAB 0.411765 0.8
151 XYA 0.411765 0.8
152 5SV 0.41129 0.785714
153 ARG AMP 0.410448 0.833333
154 G3A 0.409091 0.851852
155 AP0 0.408759 0.875
156 LPA AMP 0.407407 0.821429
157 2A5 0.40678 0.825
158 A2R 0.406504 0.858974
159 1ZZ 0.40625 0.8
160 4UU 0.406015 0.897436
161 G5P 0.406015 0.851852
162 5AL 0.404959 0.883117
163 TXD 0.404412 0.886076
164 G G G RPC 0.404255 0.898734
165 NAD IBO 0.404255 0.897436
166 7D3 0.403509 0.8125
167 MAP 0.403226 0.82716
168 G G 0.403101 0.886076
169 LA8 ALF 3PG 0.40146 0.841463
170 ALF ADP 3PG 0.40146 0.841463
171 P1H 0.401316 0.855422
172 AHZ 0.4 0.821429
173 OOB 0.4 0.907895
174 9SN 0.4 0.851852
175 NDP 0.4 0.898734
176 NPW 0.4 0.865854
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4NKT; Ligand: 2KH; Similar sites found: 26
This union binding pocket(no: 1) in the query (biounit: 4nkt.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5TVI MYR 0.003758 0.47265 None
2 4XJ6 GH3 0.00003533 0.49801 2.93255
3 3ER9 3AT 0.005327 0.41242 3.0303
4 3KRU FMN 0.0109 0.41979 3.81232
5 2Q8H TF4 0.03849 0.4024 4.10557
6 1JGS SAL 0.01187 0.43045 4.34783
7 2HHP FLC 0.005537 0.42256 4.39883
8 1GJW GLC 0.01736 0.40697 4.39883
9 3JYY PPV 0.002125 0.45035 4.87805
10 5EB4 FAD 0.02358 0.41145 5.27859
11 1W3T 3GR 0.01622 0.41649 6.12245
12 1R89 CTP 0.003913 0.40984 6.86499
13 4U03 GTP 0.00009288 0.40952 7.03812
14 3JZ0 APC 0.002069 0.43336 8.36237
15 1Q79 3AT 0.002312 0.43113 9.38416
16 4JLZ UTP 0.002822 0.44098 10.5572
17 3N7S 3N7 0.0006675 0.48689 13.913
18 1UO5 PIH 0.0274 0.40485 17.6471
19 3HIY UTP 0.000000001506 0.70501 19.6481
20 2B56 U5P 0.0000000692 0.52196 25.5132
21 2B56 UTP 0.0000000692 0.52196 25.5132
22 5I49 2KH 0.00000001851 0.67701 28.739
23 5A2Z GTP 0.00000002976 0.67852 36.9501
24 3HJ1 UTP 0.000000001321 0.68746 38.1232
25 2Q0D ATP 0.00000000024 0.78607 38.8102
26 5W0N 2KH 0.00000000008827 0.7365 49.2669
Pocket No.: 2; Query (leader) PDB : 4NKT; Ligand: 2KH; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 4nkt.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1VPD TLA 0.03207 0.40031 2.00669
2 3RV5 DXC 0.04169 0.40388 2.24719
3 2P3V SRT 0.01435 0.41161 2.73438
4 4RM0 FUC NAG GAL 0.01641 0.40718 3.48101
5 4ICS TRP GLY 0.01732 0.4003 3.81232
6 3ACT BGC 0.02469 0.40256 4.39883
7 4OAV PUP 0.02764 0.4032 4.69208
8 2JFV FLC 0.01178 0.42218 4.811
9 4BC5 5FX 0.01615 0.40849 4.98534
10 3DTU DXC 0.02949 0.40084 5.34351
11 5CX6 CDP 0.02799 0.40096 7.03812
12 5OCA 9QZ 0.03646 0.407 13.0252
13 1UO4 PIH 0.01295 0.40867 17.6471
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