Receptor
PDB id Resolution Class Description Source Keywords
1R89 1.8 Å EC: 2.7.7.25 CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS I CCA-ADDING ENZYME NUCLEOTIDE COMPLEXES ARCHAEOGLOBUS FULGIDUS CCA ADDING ENZYME INCOMING NUCLEOTIDE NUCLEOTIDYLTRANSFERASUPERFAMILY TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS I CCA-ADDIN AND ITS NUCLEOTIDE COMPLEXES MOL.CELL V. 12 1165 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:633;
Invalid;
none;
submit data
35.453 Cl [Cl-]
CTP A:501;
A:502;
Valid;
Valid;
none;
none;
submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
MG A:750;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
MN A:600;
A:601;
A:604;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
NA A:603;
Part of Protein;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1R89 1.8 Å EC: 2.7.7.25 CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS I CCA-ADDING ENZYME NUCLEOTIDE COMPLEXES ARCHAEOGLOBUS FULGIDUS CCA ADDING ENZYME INCOMING NUCLEOTIDE NUCLEOTIDYLTRANSFERASUPERFAMILY TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS I CCA-ADDIN AND ITS NUCLEOTIDE COMPLEXES MOL.CELL V. 12 1165 2003
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1R8B - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 1R89 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
3 1R8C - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1R8B - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 1R89 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
3 1R8C - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1R8B - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 1R89 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
3 1R8C - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CTP; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 CTP 1 1
2 CDP 0.895522 1
3 CAR 0.753623 0.985507
4 C 0.753623 0.985507
5 C5P 0.753623 0.985507
6 7XL 0.74026 0.944444
7 C2G 0.734177 0.957747
8 C5G 0.702381 0.944444
9 CDM 0.690476 0.894737
10 CDC 0.678571 0.82716
11 CXY 0.674419 0.944444
12 CDP MG 0.662338 0.90411
13 UTP 0.620253 0.942029
14 1AA 0.617021 0.906667
15 DCP 0.609756 0.90411
16 CTN 0.608696 0.857143
17 AR3 0.608696 0.857143
18 91P 0.582524 0.851852
19 I5A 0.577465 0.816901
20 C C 0.568182 0.929577
21 UDP 0.54321 0.942029
22 2AA 0.542056 0.693878
23 MCN 0.542056 0.819277
24 C3P 0.538462 0.942857
25 YYY 0.52381 0.90411
26 PMT 0.52381 0.85
27 GCQ 0.523256 0.90411
28 CSQ 0.520408 0.905405
29 CSV 0.520408 0.905405
30 16B 0.518519 0.917808
31 PCD 0.517544 0.781609
32 C2P 0.5 0.957143
33 GPC 0.495575 0.819277
34 FN5 0.495413 0.871795
35 CSF 0.491071 0.871795
36 DKZ 0.481013 0.746667
37 8GT 0.473118 0.907895
38 UNP 0.47191 0.915493
39 TKW 0.46988 0.971429
40 H6Y 0.463158 0.855263
41 5HM 0.458824 0.958333
42 G C 0.45614 0.8375
43 MGT 0.453608 0.829268
44 UDH 0.452632 0.844156
45 UPP 0.452632 0.888889
46 UFM 0.447917 0.888889
47 GDU 0.447917 0.888889
48 GUD 0.447917 0.888889
49 UPG 0.447917 0.888889
50 DCM 0.447059 0.890411
51 DC 0.447059 0.890411
52 UFG 0.434343 0.842105
53 U2F 0.434343 0.842105
54 UPF 0.434343 0.842105
55 U5P 0.433735 0.927536
56 URM 0.43299 0.876712
57 660 0.43299 0.876712
58 UP5 0.432432 0.857143
59 5GW 0.431579 0.890411
60 UPU 0.430108 0.887324
61 U A C C 0.428571 0.846154
62 C5P SIA 0.423729 0.893333
63 DOC 0.423529 0.890411
64 G3N 0.421569 0.890411
65 G G G C 0.421488 0.85
66 G8D 0.421053 0.907895
67 UDX 0.42 0.888889
68 UAD 0.42 0.888889
69 A G C C 0.418033 0.848101
70 2KH 0.417582 0.915493
71 3UC 0.417476 0.842105
72 4GW 0.415842 0.866667
73 UGA 0.411765 0.901408
74 V12 0.411765 0.75
75 UGB 0.411765 0.901408
76 USQ 0.411765 0.780488
77 CG2 0.410256 0.873418
78 GEO 0.407407 0.783784
79 G C C C 0.404762 0.860759
80 NVG 0.403846 0.731707
81 44P 0.402299 0.902778
82 8OD 0.402062 0.855263
83 A U C C 0.4 0.835443
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1R89; Ligand: CTP; Similar sites found: 203
This union binding pocket(no: 1) in the query (biounit: 1r89.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO4 PIH 0.007944 0.4403 None
2 1UO5 PIH 0.01539 0.43394 None
3 2W8Q SIN 0.00448 0.42948 1.14416
4 3HZL 6PC 0.02395 0.40829 1.51134
5 1KC7 PPR 0.0167 0.40339 1.60183
6 1O9U ADZ 0.0203 0.41188 1.71429
7 1O68 KIV 0.004645 0.41089 1.81818
8 2PT9 S4M 0.004048 0.40492 1.86916
9 2PT9 2MH 0.007707 0.40492 1.86916
10 1KTC NGA 0.002764 0.42009 1.97531
11 2V7T SAH 0.03729 0.40893 2.00669
12 4CIB 7UZ 0.0005854 0.45437 2.0595
13 3ZPG 5GP 0.0008023 0.48128 2.09424
14 1VDC FAD 0.01598 0.4047 2.1021
15 4M51 BEZ 0.02355 0.4023 2.10773
16 4R33 SAH 0.003874 0.41521 2.14286
17 4R33 TRP 0.003874 0.41521 2.14286
18 2NCD ADP 0.009499 0.40322 2.14286
19 2DKH FAD 0.002733 0.42101 2.19092
20 2DKH 3HB 0.008168 0.40925 2.19092
21 2HFK E4H 0.002498 0.42189 2.19436
22 1EYQ NAR 0.005024 0.40443 2.25225
23 3CQD ATP 0.006915 0.41003 2.26537
24 2ZWS PLM 0.03308 0.41573 2.28833
25 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.008918 0.40872 2.28833
26 1GJW MAL 0.004841 0.4003 2.28833
27 1M1B SPV 0.001658 0.43529 2.37288
28 2JFV FLC 0.01175 0.40461 2.4055
29 3P7I P7I 0.002755 0.42015 2.49221
30 2PP3 LGT 0.002308 0.40319 2.51256
31 4O8A 2OP 0.001987 0.46184 2.51716
32 1Q11 TYE 0.002845 0.41958 2.68817
33 3Q9T FAY 0.007763 0.40911 2.746
34 3K5X P8D 0.003917 0.40383 2.746
35 1NW5 SAM 0.001012 0.41795 2.82132
36 4JRB PGT 0.003517 0.40098 2.88462
37 1UXG NAD 0.002912 0.42575 2.91262
38 1UXG FUM 0.002912 0.42575 2.91262
39 4OYA 1VE 0.02178 0.42265 2.97483
40 1H0C AOA 0.01122 0.4113 2.97483
41 2BGM NAJ 0.01592 0.41064 2.97483
42 1I0Z OXM 0.02548 0.40695 2.97483
43 4IOK ADP 0.005275 0.40215 2.97483
44 4B16 NAG 0.03598 0.40613 3.00752
45 2BZ1 TAU 0.01306 0.43784 3.06122
46 3U4C NDP 0.001036 0.4315 3.20285
47 2YIV YIV 0.00221 0.4511 3.20366
48 2YIV NBN 0.002982 0.43752 3.20366
49 3TKA CTN 0.04104 0.41147 3.20366
50 4KCF AKM 0.002955 0.40672 3.20366
51 5EQU AKG 0.02447 0.4015 3.20366
52 1ZJ6 G3D 0.001903 0.41087 3.20856
53 1WRA PC 0.01047 0.41266 3.24675
54 2Q0D ATP 0.0005287 0.47574 3.39943
55 3P3N AKG 0.01032 0.40709 3.4384
56 3CBG 4FE 0.006085 0.44629 3.44828
57 3G6M CFF 0.01672 0.40557 3.44828
58 2VQ5 HBA 0.01058 0.41245 3.48259
59 3IHB GLU 0.001173 0.45594 3.66133
60 3IHB TRS 0.02632 0.44742 3.66133
61 2C31 ADP 0.01579 0.41817 3.66133
62 2C31 TZD 0.01627 0.41817 3.66133
63 1R27 MGD 0.008019 0.40646 3.66133
64 1XHL NDP 0.007558 0.4029 3.7037
65 1T26 GBD 0.02813 0.41606 3.72671
66 1T26 NAI 0.02813 0.41606 3.72671
67 1E7S NAP 0.003619 0.41509 3.73832
68 4K30 NLG 0.006522 0.40486 3.75
69 3O03 NAP 0.01394 0.41302 3.78007
70 1QJC PNS 0.01372 0.41083 3.79747
71 1GSA ADP 0.00293 0.40512 3.79747
72 2Q37 3AL 0.009458 0.4033 3.8674
73 4USQ FAD 0.003558 0.41783 3.87812
74 2XVE FAD 0.00577 0.43163 3.89016
75 4ME6 ADP 0.006113 0.41133 3.89016
76 2WQP WQP 0.001354 0.42409 4.01146
77 4EXO PYR 0.006764 0.42808 4.10959
78 3QV9 QV7 0.002973 0.42457 4.11899
79 2XDQ MGX 0.005762 0.439 4.13043
80 4PLG OXM 0.008195 0.40715 4.19162
81 4PLG NAI 0.008195 0.40715 4.19162
82 1H16 PYR 0.01027 0.41947 4.21607
83 2PWY SAH 0.002356 0.41031 4.26357
84 3ZGE ASP 0.002781 0.44637 4.34783
85 1C7S CBS 0.0009592 0.42188 4.34783
86 4GQB 0XU 0.01307 0.41133 4.34783
87 1SOW NAD 0.006286 0.40595 4.34783
88 3GM5 CIT 0.0002039 0.48174 4.40252
89 1TDF NAP 0.01964 0.41413 4.43038
90 1TDF FAD 0.01614 0.40373 4.43038
91 2Q1A 2KT 0.008122 0.41166 4.43686
92 1JAC AMG 0.006201 0.44587 4.51128
93 4GYW UDP 0.0008513 0.43902 4.57666
94 2VDJ HSE 0.01004 0.41994 4.65116
95 2Y6P CTP 0.001702 0.41766 4.70085
96 1Z42 HBA 0.001708 0.49277 4.73373
97 1Z44 NPO 0.01299 0.43797 4.73373
98 1KOL NAD 0.004925 0.41468 4.77387
99 3MAG 3MA 0.009773 0.43564 4.80549
100 2C7G ODP 0.00717 0.42349 4.80549
101 2C7G FAD 0.007471 0.42349 4.80549
102 1FW1 GSH 0.0009146 0.41763 4.80549
103 3MCT 3MC 0.004506 0.41143 4.80549
104 2QJN KDG 0.001758 0.40744 4.80549
105 9LDT OXM 0.006946 0.44332 4.81928
106 9LDB OXM 0.0277 0.41209 4.81928
107 4FGC PQ0 0.004352 0.41758 4.84848
108 2FWP ICR 0.005666 0.41121 4.91803
109 1YOA FMN 0.008333 0.44846 5.03145
110 3IOI 1GW 0.003253 0.41686 5.03356
111 3BHO B4P 0.00883 0.43792 5.03433
112 2Y7P SAL 0.003752 0.41468 5.04587
113 3MD0 GDP 0.003964 0.4085 5.07042
114 4OAG ADP 0.0009612 0.43683 5.07463
115 4RJK PYR 0.009517 0.42105 5.26316
116 1DSS NAD 0.0007178 0.43265 5.40541
117 2VAR KDF 0.001591 0.41375 5.43131
118 2BO4 FLC 0.008626 0.41651 5.54156
119 4NTD FAD 0.01006 0.40469 5.58824
120 2XK9 XK9 0.004688 0.41323 5.59006
121 1GPJ CIT 0.006329 0.41642 5.72082
122 1JH7 UVC 0.00186 0.43318 5.82011
123 1C1L GAL BGC 0.007449 0.41941 5.83942
124 1HFA PIO 0.001211 0.49917 5.88235
125 1RYD GLC 0.003031 0.43044 5.94315
126 3R35 4CO 0.005754 0.40617 5.96026
127 2F2U M77 0.002238 0.41312 5.97015
128 1P72 THM 0.003796 0.41447 5.98802
129 1ULE GLA GAL NAG 0.004165 0.43806 6
130 1RYI GOA 0.01047 0.44398 6.02094
131 4NAO AKG 0.01428 0.40651 6.13497
132 1B74 DGN 0.01035 0.41932 6.29921
133 1H8G CHT 0.01736 0.43109 6.31579
134 2HW1 FRU 0.006074 0.41145 6.37584
135 1ECM TSA 0.003818 0.40914 6.42202
136 2WGC SIA GAL BGC 0.0244 0.423 6.43275
137 1WGC SIA GAL BGC 0.02978 0.41044 6.43275
138 1I2B UPG 0.006643 0.42485 6.63616
139 1I2B USQ 0.006643 0.42485 6.63616
140 1I2B NAD 0.006643 0.42485 6.63616
141 4N7C AEF 0.007572 0.41909 6.81818
142 4NKT 2KH 0.003913 0.40984 6.86499
143 2Q09 DI6 0.001733 0.42268 6.97115
144 3QDW NDG 0.0012 0.4555 6.99301
145 3QDY A2G GAL 0.0046 0.43602 6.99301
146 3QDT A2G GAL 0.005562 0.43212 6.99301
147 3QDY CBS 0.01811 0.40178 6.99301
148 1T3D CYS 0.002629 0.44001 7.09382
149 4WBD ADP 0.004087 0.43129 7.09382
150 4WBD CIT 0.01034 0.41933 7.09382
151 3U5S FAD 0.001437 0.41446 7.14286
152 3PNA CMP 0.003285 0.41172 7.14286
153 1FIQ SAL 0.007715 0.40255 7.14286
154 4W6Z ETF 0.02326 0.40893 7.20461
155 2ZJ5 ADP 0.009045 0.40413 7.32265
156 2YD6 FLC 0.0006448 0.51097 7.54717
157 1BTN I3P 0.001354 0.50254 7.54717
158 3CH5 GDP 0.001794 0.41182 7.69231
159 1H2M OGA 0.01351 0.40194 7.69231
160 3CF6 SP1 0.002106 0.40025 7.78443
161 1JGS SAL 0.00119 0.49433 7.97101
162 2YVF NAD 0.01194 0.41848 8.00915
163 2YVF FAD 0.01152 0.41848 8.00915
164 3WUD GLC GAL 0.0253 0.40081 8.08823
165 4M5P 23W 0.008698 0.4229 8.10811
166 4INB 1F6 0.002473 0.40408 8.21918
167 2ZE3 AKG 0.006618 0.40987 8.23799
168 4K7O EKZ 0.01426 0.40654 8.33333
169 4TSK NDP 0.009151 0.42057 8.46682
170 3IB9 BTN 0.007055 0.42377 8.69565
171 3BL6 FMC 0.002637 0.4011 8.69565
172 1XX4 BAM 0.001501 0.46786 9.57854
173 3UEC ALA ARG TPO LYS 0.000775 0.46413 9.58904
174 4G1V FAD 0.001847 0.42061 9.77444
175 3SQG COM 0.01241 0.43025 9.83982
176 1XE7 GUN 0.01247 0.42241 9.85222
177 3BY8 MLT 0.01885 0.40098 9.85915
178 1Q79 3AT 0.0007635 0.45581 10.0687
179 1Q3Q ANP 0.01841 0.40802 10.7551
180 2HGZ PBF 0.001861 0.41574 11.4379
181 1T0S BML 0.01781 0.4081 11.6279
182 1WHT BZS 0.00147 0.4442 11.7647
183 1V7R CIT 0.04052 0.40342 12.3656
184 2X2T GAL NGA 0.007298 0.43393 12.4183
185 1SC3 MLI 0.022 0.40371 12.5
186 2O66 FLC 0.004278 0.41789 12.5926
187 1NN5 ANP 0.002356 0.41952 13.0233
188 1NN5 2DT 0.002356 0.41952 13.0233
189 3PJU C2E 0.006022 0.40001 13.253
190 1QO0 BMD 0.004128 0.42456 13.7755
191 3I6B KDO 0.007393 0.40264 13.8889
192 4JCA CIT 0.01767 0.42228 14.3713
193 3S9K CIT 0.000237 0.54713 15.2542
194 1YAG ATP 0.002565 0.40896 16
195 4HZO COA 0.005444 0.40807 16.3522
196 3E81 SLB 0.003107 0.42376 16.4634
197 1QH9 LAC 0.005971 0.41753 16.8103
198 1NP0 NGT 0.01044 0.40688 18.9474
199 1SS4 CIT 0.01232 0.46273 20.2614
200 1SS4 GSH 0.01445 0.43431 20.2614
201 1NU4 MLA 0.0168 0.43187 20.6186
202 3GEG NAD 0.005703 0.40231 22.2672
203 2XI7 XI7 0.01955 0.42826 24.4565
Pocket No.: 2; Query (leader) PDB : 1R89; Ligand: CTP; 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: 1r89.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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