Receptor
PDB id Resolution Class Description Source Keywords
2VBU 1.7 Å EC: 2.7.1.161 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP METHANOCOCCUS JANNASCHII TRANSFERASE CRADLE-LOOP BARREL CTP-DEPENDENT KINASE FMN
Ref.: A CTP-DEPENDENT ARCHAEAL RIBOFLAVIN KINASE FORMS A BRIDGE IN THE EVOLUTION OF CRADLE-LOOP BARRELS. STRUCTURE V. 15 1577 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDP A:1133;
 Valid;
 none;
 submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
MG A:1134;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
MRD A:1135;
A:1136;
A:1137;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
118.174 C6 H14 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VBU 1.7 Å EC: 2.7.1.161 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP METHANOCOCCUS JANNASCHII TRANSFERASE CRADLE-LOOP BARREL CTP-DEPENDENT KINASE FMN
Ref.: A CTP-DEPENDENT ARCHAEAL RIBOFLAVIN KINASE FORMS A BRIDGE IN THE EVOLUTION OF CRADLE-LOOP BARRELS. STRUCTURE V. 15 1577 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VBU - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VBV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VBU - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VBV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VBU - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VBV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
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 : 2VBU; Ligand: CDP; Similar sites found: 67
This union binding pocket(no: 1) in the query (biounit: 2vbu.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5M6N 7H9 0.01708 0.42867 None
2 3B6C SDN 0.01826 0.42457 None
3 4XG0 CIT 0.02593 0.41529 None
4 5C2N NAG 0.03852 0.40818 None
5 1H8P PC 0.03014 0.40797 None
6 2ALG DAO 0.04073 0.40611 None
7 1J78 OLA 0.03922 0.42024 2.20588
8 3LL9 ADP 0.01137 0.41531 2.20588
9 2GNB MAN 0.03926 0.40954 2.94118
10 2JCB ADP 0.009945 0.42971 3.5
11 1YXM ADE 0.00896 0.44657 3.67647
12 3SE5 ANP 0.004643 0.43383 3.67647
13 4PPF FLC 0.04462 0.40277 3.67647
14 1GXU 2HP 0.000134 0.55972 4.3956
15 5GVR LMR 0.01055 0.42482 4.41176
16 2JBH 5GP 0.02236 0.41563 4.41176
17 1F28 UMP 0.01509 0.4129 4.41176
18 1JI0 ATP 0.04842 0.40161 4.41176
19 2CBZ ATP 0.008012 0.45408 5.14706
20 1TLC DGP 0.003356 0.44908 5.14706
21 1TDU DUR 0.0147 0.4252 5.14706
22 1AXW UMP 0.01289 0.41998 5.14706
23 2A9W UMP 0.03186 0.41197 5.14706
24 1DDU DDU 0.02872 0.40991 5.14706
25 4RW3 SHV 0.03164 0.40243 5.14706
26 4FUA PGH 0.0241 0.41808 5.88235
27 4CVN ADP 0.02485 0.41735 5.88235
28 1D8C GLV 0.04494 0.41407 5.88235
29 5TCI MLI 0.02461 0.40657 5.88235
30 4K6B GLU 0.04248 0.40472 6.61765
31 1NB9 ADP 0.0002813 0.44452 7.35294
32 1NB9 RBF 0.0002813 0.44452 7.35294
33 4WZ6 ATP 0.03012 0.41597 7.35294
34 2X7I CIT 0.02734 0.40722 7.35294
35 1RRV TYD 0.0204 0.4 7.35294
36 3FIU POP 0.01744 0.42967 8.08823
37 3I6B KDO 0.01839 0.42441 8.08823
38 3LRE ADP 0.03463 0.4147 8.08823
39 2DPY ADP 0.02909 0.41365 8.08823
40 1N07 FMN 0.001493 0.41107 8.08823
41 1M2Z BOG 0.03369 0.40882 8.08823
42 4NAE 1GP 0.03505 0.40726 8.08823
43 3NHB ADP 0.04624 0.40548 8.08823
44 2NUO BGC 0.03688 0.41429 8.19672
45 2NU5 NAG 0.04226 0.40599 8.19672
46 2HYR BGC GLC 0.04484 0.40456 8.19672
47 1JJ7 ADP 0.02233 0.42793 8.82353
48 1G6H ADP 0.02305 0.42716 8.82353
49 5CX8 TG6 0.03851 0.40442 8.82353
50 2AWN ADP 0.00533 0.46572 9.55882
51 2W58 ADP 0.006727 0.45891 9.55882
52 5GJC ATP 0.02826 0.40648 10.2941
53 5H2U 1N1 0.01766 0.40956 11.0294
54 5FUI APY 0.03935 0.40902 11.3636
55 2QQD AG2 0.02666 0.4157 11.6071
56 1DCP HBI 0.01669 0.43396 12.5
57 3QDW NDG 0.04273 0.40876 13.9706
58 2OBM ADP 0.009442 0.44525 15.4412
59 1GOJ ADP 0.0312 0.41803 15.4412
60 5A89 FMN 0.00006813 0.42267 17.6471
61 5A89 ADP 0.00006813 0.42267 17.6471
62 1EXF GLY 0.01544 0.41877 17.6471
63 2QES ADE 0.03694 0.41133 17.6471
64 2IU8 PLM 0.01263 0.40057 19.1176
65 2XN5 FUN 0.007241 0.43674 19.8529
66 4AG5 ADP 0.04389 0.40598 19.8529
67 5H4I 7HQ 0.008707 0.42463 21.3235
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