Receptor
PDB id Resolution Class Description Source Keywords
5CX6 2.1 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF THOSEA ASIGNA VIRUS RNA-DEPENDENT RNA P (RDRP) COMPLEXED WITH CDP THOSEA ASIGNA VIRUS RDRP COMPLEX CDP TRANSFERASE
Ref.: THE STRUCTURE OF THE RNA-DEPENDENT RNA POLYMERASE O PERMUTOTETRAVIRUS SUGGESTS A LINK BETWEEN PRIMER-DE AND PRIMER-INDEPENDENT POLYMERASES. PLOS PATHOG. V. 11 05265 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:701;
B:705;
A:702;
B:702;
B:703;
A:706;
B:701;
B:704;
A:707;
A:705;
A:704;
A:703;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
MG A:720;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
CDP B:713;
A:721;
Valid;
Valid;
none;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
GOL A:714;
A:713;
A:712;
A:709;
B:706;
A:717;
A:719;
B:709;
A:711;
A:708;
B:707;
B:712;
A:710;
B:710;
A:716;
B:708;
A:715;
B:711;
A:718;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CX6 2.1 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF THOSEA ASIGNA VIRUS RNA-DEPENDENT RNA P (RDRP) COMPLEXED WITH CDP THOSEA ASIGNA VIRUS RDRP COMPLEX CDP TRANSFERASE
Ref.: THE STRUCTURE OF THE RNA-DEPENDENT RNA POLYMERASE O PERMUTOTETRAVIRUS SUGGESTS A LINK BETWEEN PRIMER-DE AND PRIMER-INDEPENDENT POLYMERASES. PLOS PATHOG. V. 11 05265 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5CX6 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5CX6 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5CX6 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CDP; Similar ligands found: 89
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 CTP 0.895522 1
3 C5P 0.787879 0.985507
4 CAR 0.787879 0.985507
5 C 0.787879 0.985507
6 7XL 0.77027 0.944444
7 C2G 0.74026 0.957747
8 CDC 0.725 0.82716
9 CDP MG 0.712329 0.90411
10 C5G 0.707317 0.944444
11 CDM 0.695122 0.894737
12 CXY 0.678571 0.944444
13 CTN 0.636364 0.857143
14 AR3 0.636364 0.857143
15 1AA 0.619565 0.906667
16 C C 0.607143 0.929577
17 UDP 0.605263 0.942029
18 I5A 0.602941 0.816901
19 YYY 0.582278 0.90411
20 GCQ 0.560976 0.90411
21 C3P 0.56 0.942857
22 MCN 0.557692 0.819277
23 PMT 0.554455 0.85
24 91P 0.553398 0.851852
25 UTP 0.54321 0.942029
26 2AA 0.542857 0.693878
27 16B 0.538462 0.917808
28 CSV 0.536842 0.905405
29 CSQ 0.536842 0.905405
30 DCP 0.535714 0.90411
31 C2P 0.519481 0.957143
32 PCD 0.517857 0.781609
33 FN5 0.509434 0.871795
34 GPC 0.509091 0.819277
35 CSF 0.504587 0.871795
36 DKZ 0.5 0.746667
37 UNP 0.488372 0.915493
38 TKW 0.4875 0.971429
39 G C 0.481818 0.8375
40 5GW 0.477778 0.890411
41 5HM 0.47561 0.958333
42 DC 0.463415 0.890411
43 DCM 0.463415 0.890411
44 U A C C 0.452174 0.846154
45 UPP 0.451613 0.888889
46 UDH 0.451613 0.844156
47 G8D 0.450549 0.907895
48 U5P 0.45 0.927536
49 C5P SIA 0.447368 0.893333
50 UPG 0.446809 0.888889
51 GUD 0.446809 0.888889
52 GDU 0.446809 0.888889
53 660 0.446809 0.876712
54 URM 0.446809 0.876712
55 UFM 0.446809 0.888889
56 8OD 0.445652 0.855263
57 G G G C 0.444444 0.85
58 UPU 0.444444 0.887324
59 4GW 0.443299 0.866667
60 A G C C 0.440678 0.848101
61 DOC 0.439024 0.890411
62 M7G 0.43617 0.829268
63 U2F 0.43299 0.842105
64 UFG 0.43299 0.842105
65 UPF 0.43299 0.842105
66 2KH 0.431818 0.915493
67 G C C C 0.42623 0.860759
68 CG2 0.421053 0.873418
69 A U C C 0.420635 0.835443
70 G3N 0.42 0.890411
71 UDP UDP 0.418605 0.885714
72 UDX 0.418367 0.888889
73 UAD 0.418367 0.888889
74 44P 0.416667 0.902778
75 3UC 0.415842 0.842105
76 M7M 0.412371 0.797619
77 8GT 0.410526 0.907895
78 V12 0.41 0.75
79 UGB 0.41 0.901408
80 USQ 0.41 0.780488
81 UGA 0.41 0.901408
82 DCP MG 0.408602 0.818182
83 UP5 0.405405 0.857143
84 GEO 0.405063 0.783784
85 CH 0.404762 0.942857
86 UDM 0.403846 0.864865
87 H6Y 0.402062 0.855263
88 NVG 0.401961 0.731707
89 CTP C C C C 0.4 0.915493
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CX6; Ligand: CDP; 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: 5cx6.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5CX6; Ligand: CDP; Similar sites found: 139
This union binding pocket(no: 2) in the query (biounit: 5cx6.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1D4D FAD 0.04097 0.41807 1.04895
2 4MRP GSH 0.005016 0.42525 1.30293
3 5AZC PGT 0.03577 0.43961 1.33333
4 3TDC 0EU 0.009836 0.43333 1.56028
5 3VCY UD1 0.02695 0.40487 1.62791
6 3WCA FPS 0.03701 0.40731 1.64384
7 2ZXG S23 0.02437 0.41243 1.70213
8 5AB1 BCD TA5 HP6 MAN 0.00724 0.41095 2
9 3BP1 GUN 0.001616 0.40716 2.06897
10 3C6K MTA 0.0266 0.42174 2.09974
11 3C6K SPD 0.0266 0.42174 2.09974
12 2RKV ZBA 0.04998 0.40727 2.21729
13 2RKV COA 0.04426 0.40727 2.21729
14 4Q9N NAI 0.04187 0.40527 2.34899
15 3CH6 NAP 0.04652 0.42103 2.44755
16 3CH6 311 0.04652 0.42103 2.44755
17 2PD4 NAD 0.03676 0.41174 2.54545
18 2PD4 DCN 0.03895 0.41033 2.54545
19 2YNC YNC 0.03994 0.41058 2.60417
20 5IR4 ZPE 0.04483 0.41344 2.61628
21 2GZ3 NAP 0.02663 0.43355 2.73224
22 4COL DTP 0.003237 0.44505 2.76498
23 5V3Y 5V8 0.002376 0.44348 2.7972
24 2WPF WPF 0.04162 0.44009 2.82828
25 2WPF FAD 0.04099 0.44009 2.82828
26 3AQT RCO 0.001736 0.43063 2.85714
27 2UUU PL3 0.008371 0.46546 2.91096
28 2UUU FAD 0.00699 0.46546 2.91096
29 3SWG EPZ 0.02783 0.40822 3.05882
30 1N07 FMN 0.01382 0.43238 3.06748
31 1N07 ADP 0.007001 0.43238 3.06748
32 1NP7 FAD 0.02284 0.41822 3.06748
33 5IF4 6AK 0.04021 0.40274 3.14465
34 2GBB CIT 0.0052 0.40271 3.20513
35 1YKD CMP 0.01017 0.42257 3.26633
36 4USF 6UI 0.03386 0.40075 3.28947
37 2GLX NDP 0.03367 0.40227 3.31325
38 2H7C COA 0.04713 0.42219 3.32103
39 1XSE NDP 0.01812 0.43601 3.38983
40 5X40 ACP 0.009652 0.42967 3.42466
41 5G5G FAD 0.04267 0.41545 3.49345
42 1ICP FMN 0.0439 0.40366 3.7234
43 4U0S ADP 0.02181 0.40094 3.77907
44 3SM2 478 0.008123 0.45213 3.78788
45 1RX0 2MC 0.02028 0.41752 3.81679
46 4ZOM 4Q3 0.003575 0.45953 4
47 3KRO DST 0.0346 0.40475 4.0146
48 3KRO IPE 0.0346 0.40475 4.0146
49 4GYW UDP 0.01003 0.44244 4.11348
50 4IEH 1E9 0.02882 0.40649 4.14201
51 2FP2 TSA 0.01569 0.41361 4.21687
52 3UPY FOM 0.01129 0.40572 4.26966
53 3UR0 SVR 0.01342 0.42624 4.27184
54 2Z7I 742 0.0434 0.43046 4.41176
55 4QWT ACD 0.02902 0.40905 4.45402
56 5TV6 PML 0.01544 0.40121 4.58333
57 5G3N X28 0.0177 0.41524 4.72441
58 4IGH FMN 0.02149 0.44579 4.83871
59 4IGH ORO 0.02149 0.44579 4.83871
60 4IGH 1EA 0.02149 0.44579 4.83871
61 2EV1 OLA 0.02169 0.41079 4.95496
62 1YUC EPH 0.009185 0.43391 5.09804
63 5EY0 GTP 0.01308 0.40855 5.10949
64 3H8V ATP 0.02217 0.40549 5.13699
65 5UGW GSH 0.006149 0.41768 5.14286
66 5B4B LP5 0.007169 0.44501 5.24194
67 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.003398 0.45366 5.26316
68 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.02775 0.41372 5.26316
69 1RQJ RIS 0.02975 0.40374 5.35117
70 1FCH TYR GLN SER LYS LEU 0.006455 0.43638 5.43478
71 1SQL GUN 0.0022 0.43536 5.47945
72 1YKI NFZ 0.01663 0.43207 5.52995
73 1YKI FMN 0.01522 0.43084 5.52995
74 1KQB FMN 0.01309 0.42536 5.52995
75 1KQB BEZ 0.01457 0.42119 5.52995
76 1YYE 196 0.02253 0.40002 5.59701
77 1OQC FAD 0.03105 0.40568 5.6
78 5HGZ ACO 0.01075 0.42956 5.76132
79 1RL4 BL5 0.00003375 0.46723 5.85106
80 4P6X HCY 0.01779 0.41031 5.88235
81 1JR8 FAD 0.008087 0.4338 5.98291
82 3V49 PK0 0.004776 0.44882 6.01504
83 1N62 FAD 0.022 0.42845 6.0241
84 2D5Z L35 0.04039 0.43543 6.16438
85 1YOK P6L 0.005843 0.45667 6.25
86 4DR9 BB2 0.01079 0.41763 6.25
87 5MW4 5JU 0.004754 0.46674 6.28743
88 3MBG FAD 0.02582 0.41112 6.47482
89 5K13 6Q7 0.01717 0.41608 6.50407
90 1ZQ9 SAM 0.01749 0.41054 6.66667
91 5V4R MGT 0.006115 0.43235 6.79012
92 3ZW2 NAG GAL FUC 0.01389 0.40501 6.89655
93 4NKT 2KH 0.02799 0.40096 7.03812
94 5L4L 7OX 0.02499 0.42473 7.23684
95 1QG6 TCL 0.03457 0.42087 7.27969
96 1QG6 NAD 0.03457 0.42087 7.27969
97 1USF FMN 0.02683 0.41358 7.30337
98 1USF NAP 0.03118 0.41358 7.30337
99 3TL1 JRO 0.007627 0.40212 7.54717
100 4JE7 BB2 0.02231 0.40526 7.61421
101 3QKD HI0 0.02381 0.41254 7.73481
102 5EYP GTP 0.03741 0.40202 7.76053
103 3Q8G PEE 0.01252 0.45294 7.8125
104 3ANP DAO 0.01162 0.42965 7.84314
105 3ANP DCC 0.01621 0.42581 7.84314
106 3UYW TAU 0.01094 0.40315 7.94393
107 2Q3O FMN 0.04079 0.40013 8.18414
108 4B7P 9UN 0.04326 0.41788 8.69565
109 1F4G TP4 0.02144 0.40573 8.71212
110 3T03 3T0 0.006332 0.43041 8.80282
111 3FUR Z12 0.003033 0.48278 8.82353
112 3H0A D30 0.001458 0.47941 8.82353
113 3G9E RO7 0.004429 0.46212 8.85609
114 2VWA PTY 0.003718 0.42459 8.91089
115 1NBU PH2 0.001242 0.41166 9.2437
116 2PT9 2MH 0.02287 0.42259 9.34579
117 2ZCQ B65 0.02184 0.4333 9.55631
118 4RC8 STE 0.03261 0.40129 10.3604
119 1LN1 DLP 0.01698 0.42937 11.215
120 3M6P BB2 0.01373 0.41417 11.399
121 3IX8 TX3 0.01547 0.42273 11.5607
122 1SR7 MOF 0.005218 0.45298 11.583
123 4RHP PEF 0.01185 0.41685 12.3404
124 2F5Z FAD 0.02808 0.42683 12.5
125 4BQS K2Q 0.004851 0.40324 12.5
126 3KP6 SAL 0.008957 0.4095 12.5828
127 2H29 DND 0.04477 0.40429 13.7566
128 3G08 FEE 0.04052 0.42381 14.1414
129 3FAL REA 0.001564 0.45895 15.0376
130 1GHE ACO 0.0261 0.40804 15.2542
131 4BKS X6C 0.008547 0.40862 15.3846
132 4TV1 36M 0.00753 0.41316 16.3347
133 2QE4 JJ3 0.04886 0.41741 16.5323
134 5U1M ACE LEU TYR ALA SER SER ASN PRO ALA PTR 0.009376 0.42671 17.1429
135 5OCA 9QZ 0.02019 0.41058 17.4603
136 5N7O 69Y 0.0247 0.40237 18.0995
137 2WCJ M21 0.0246 0.40933 20.5674
138 3RV5 DXC 0.03515 0.40583 22.4719
139 3N7S 3N7 0.01176 0.40966 27.0833
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