Receptor
PDB id Resolution Class Description Source Keywords
2V2V 2.4 Å EC: 2.7.1.148 ISPE IN COMPLEX WITH LIGAND AQUIFEX AEOLICUS TRANSFERASE 4-DIPHOSPHOCYTIDYL-2C-METHYL-D- ERYTHRITOL AQUIFEX AEOLICUS NUCLEOTIDE-BINDING ISOPRENE BIOSYNTHESIS KINASE ATP-BINDING NON-MEVALONATE
Ref.: SYNTHESIS AND CHARACTERIZATION OF CYTIDINE DERIVATIVES THAT INHIBIT THE KINASE ISPE OF THE NON-MEVALONATE PATHWAY FOR ISOPRENOID BIOSYNTHESIS. CHEMMEDCHEM V. 3 91 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BR A:1272;
A:1273;
A:1274;
A:1275;
A:1276;
B:1274;
B:1275;
B:1276;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
79.904 Br [Br-]
GOL A:1271;
B:1272;
B:1273;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:1269;
A:1270;
B:1269;
B:1270;
B:1271;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
V12 A:1277;
B:1277;
Valid;
Valid;
none;
none;
Ki = 85.8 uM
400.389 C18 H20 N6 O5 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2V2V 2.4 Å EC: 2.7.1.148 ISPE IN COMPLEX WITH LIGAND AQUIFEX AEOLICUS TRANSFERASE 4-DIPHOSPHOCYTIDYL-2C-METHYL-D- ERYTHRITOL AQUIFEX AEOLICUS NUCLEOTIDE-BINDING ISOPRENE BIOSYNTHESIS KINASE ATP-BINDING NON-MEVALONATE
Ref.: SYNTHESIS AND CHARACTERIZATION OF CYTIDINE DERIVATIVES THAT INHIBIT THE KINASE ISPE OF THE NON-MEVALONATE PATHWAY FOR ISOPRENOID BIOSYNTHESIS. CHEMMEDCHEM V. 3 91 2008
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2V8P - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VF3 - GVS C17 H22 N4 O6 S CCOC(=O)CC....
3 2V34 - CTN C9 H13 N3 O5 C1=CN(C(=O....
4 2V2Z - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
5 2V2Q Ki = 712 uM NVG C19 H22 N6 O5 c1ccc2c(c1....
6 2V2V Ki = 85.8 uM V12 C18 H20 N6 O5 c1ccc2c(c1....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2V8P - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VF3 - GVS C17 H22 N4 O6 S CCOC(=O)CC....
3 2V34 - CTN C9 H13 N3 O5 C1=CN(C(=O....
4 2V2Z - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
5 2V2Q Ki = 712 uM NVG C19 H22 N6 O5 c1ccc2c(c1....
6 2V2V Ki = 85.8 uM V12 C18 H20 N6 O5 c1ccc2c(c1....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2V8P - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 2VF3 - GVS C17 H22 N4 O6 S CCOC(=O)CC....
3 2V34 - CTN C9 H13 N3 O5 C1=CN(C(=O....
4 2V2Z - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
5 2V2Q Ki = 712 uM NVG C19 H22 N6 O5 c1ccc2c(c1....
6 2V2V Ki = 85.8 uM V12 C18 H20 N6 O5 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: V12; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 V12 1 1
2 NVG 0.758242 0.972603
3 I5A 0.482353 0.794521
4 CTN 0.470588 0.833333
5 AR3 0.470588 0.833333
6 C5P 0.43617 0.7375
7 C 0.43617 0.7375
8 CAR 0.43617 0.7375
9 CTP 0.411765 0.75
10 CDP 0.41 0.75
11 CDP MG 0.405941 0.719512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V2V; Ligand: V12; Similar sites found: 77
This union binding pocket(no: 1) in the query (biounit: 2v2v.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WUW TSU 0.01791 0.44382 None
2 3GJ0 GDP 0.04136 0.40566 1.35747
3 3GJ8 GDP 0.04033 0.40286 1.35747
4 3HYW DCQ 0.04921 0.40513 1.47601
5 1W2D ADP 0.03397 0.41019 1.50943
6 1JJ7 ADP 0.002732 0.48688 1.53846
7 4K7O EKZ 0.04882 0.40871 1.78571
8 4IEE AGS 0.04045 0.40977 2.21402
9 2POC UD1 0.0496 0.40494 2.21402
10 2BES RES 0.03649 0.40511 2.32558
11 4WZ6 ATP 0.007377 0.45547 2.58303
12 2X5F PLP 0.03871 0.40719 2.95203
13 4HSE ADP 0.0357 0.40561 2.95203
14 1FNN ADP 0.02282 0.40281 2.95203
15 2PL3 ADP 0.01664 0.4306 2.9661
16 5SXS NIZ 0.0289 0.42481 3.32103
17 2CBZ ATP 0.004376 0.46989 3.37553
18 1SQL GUN 0.04698 0.41332 3.42466
19 2W58 ADP 0.004082 0.4647 3.46535
20 1G8S MET 0.006935 0.46074 3.47826
21 3PQC GDP 0.0225 0.42775 3.58974
22 2DPY ADP 0.02561 0.42464 3.69004
23 2PVF ACP 0.03042 0.40273 3.69004
24 3AIH BMA MAN MAN 0.04105 0.40989 4.03226
25 3LRE ADP 0.003769 0.48139 4.05904
26 2C04 GCP 0.0126 0.41819 4.05904
27 1WUU ANP 0.00004702 0.40126 4.05904
28 1G3Q ADP 0.01066 0.43257 4.21941
29 1V8K ANP 0.04869 0.40189 4.42804
30 3B5J 12D 0.02084 0.42959 4.52675
31 3P48 DUP 0.02726 0.41166 4.7619
32 2OBM ADP 0.02024 0.43635 4.79705
33 1P4V GLY 0.04364 0.41305 4.79705
34 2IL4 COA 0.02589 0.40618 4.85437
35 4QOS ADP 0.03102 0.40544 4.90566
36 4BQS ADP 0.0269 0.41554 5.11364
37 3NHB ADP 0.003766 0.47403 5.16605
38 4AG5 ADP 0.003694 0.47333 5.16605
39 4LC1 GDP 0.02263 0.4195 5.16605
40 3AB4 THR 0.0305 0.41642 5.16605
41 4A4Z ANP 0.03286 0.41096 5.16605
42 5C79 PBU 0.0129 0.4454 5.33333
43 1BO4 COA 0.02144 0.42074 5.35714
44 1G6H ADP 0.002763 0.48524 5.44747
45 3B7G ANP 0.03636 0.40519 5.65217
46 3Q9L ATP 0.01692 0.41203 6.15385
47 1JI0 ATP 0.006915 0.45592 6.66667
48 3GJ7 GDP 0.03944 0.40675 7.14286
49 1GOJ ADP 0.003379 0.48532 7.74908
50 1SNN 5RP 0.03281 0.4075 7.92952
51 4CVN ADP 0.01519 0.43715 8.0292
52 3FKQ ATP 0.0244 0.40437 8.0429
53 2R42 FPS 0.0001338 0.50258 8.11808
54 1TUU ADP 0.03124 0.41986 8.48709
55 1GCK ASP PLP 0.02265 0.40014 8.48709
56 2HFU MEV 0.0007715 0.51051 8.85609
57 5BQ5 ADP BEF 0.01006 0.43001 8.99471
58 2AWN ADP 0.00121 0.50789 9.22509
59 3F81 STT 0.02835 0.42482 9.83607
60 4XG0 CIT 0.02978 0.42473 10.7728
61 3CH8 PRO GLN PRO VAL ASP SER TRP VAL 0.007204 0.44554 11.7949
62 2ZV2 609 0.04569 0.40336 12.9151
63 1GXU 2HP 0.002593 0.46947 13.1868
64 3B9Q MLI 0.0006179 0.54033 13.6531
65 4PPF FLC 0.002011 0.49214 14.0221
66 2NUN ADP 0.04552 0.40698 14.0221
67 2A2C ADP 0.0001141 0.44023 14.3911
68 2A2C NG1 0.0001141 0.44023 14.3911
69 5SWI BMA 0.01483 0.4169 15.4982
70 3ZS9 ADP ALF 0.0115 0.40527 15.4982
71 1H74 ADP 0.0000009496 0.54216 16.5541
72 1H74 ILE 0.000006742 0.52646 16.5541
73 1QHH ATP 0.02613 0.4126 19.1617
74 1A8S PPI 0.04039 0.40863 21.0332
75 2YPI PGA 0.03786 0.4077 21.0526
76 5FTB ANP 0.03176 0.40493 21.7712
77 1SQ5 ADP 0.009019 0.43629 22.1402
Pocket No.: 2; Query (leader) PDB : 2V2V; Ligand: V12; Similar sites found: 38
This union binding pocket(no: 2) in the query (biounit: 2v2v.bio2) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OAS 2SW 0.01744 0.41895 None
2 1LNX URI 0.04301 0.41252 None
3 3LL5 IP8 0.03032 0.4232 1.60643
4 2DTJ THR 0.04835 0.40289 1.68539
5 3LST SAH 0.03831 0.40488 1.84502
6 1M2Z BOG 0.0235 0.44139 1.94553
7 2GN3 MAN 0.03933 0.4054 2.38095
8 1SJN DUP 0.006103 0.43425 2.94118
9 2Q7D ANP 0.008331 0.407 2.95203
10 5TAR GDP 0.01509 0.41864 3.24324
11 2NCD ADP 0.02155 0.43301 3.32103
12 4UP4 NDG 0.03935 0.40732 3.32103
13 4UP4 NAG 0.03935 0.40732 3.32103
14 2WVZ KIF 0.04531 0.40108 3.32103
15 1G7C 5GP 0.048 0.40306 3.69004
16 3N5C GDP 0.0363 0.40953 4.32099
17 4PU5 ANP 0.01103 0.40972 4.42804
18 3VX3 ADP 0.02538 0.40152 4.43548
19 4JZ8 CIT 0.03651 0.41357 4.79705
20 4LED XXR 0.01495 0.42188 4.85075
21 3DEF GDP 0.02698 0.40618 5.72519
22 2UVO NDG 0.03758 0.4163 5.84795
23 1QH5 GSH 0.0397 0.41311 6.15385
24 2ZFI ADP 0.0376 0.40872 6.27306
25 1M0S CIT 0.03307 0.41539 6.39269
26 1G6O ADP 0.03398 0.40431 7.01107
27 4RW3 SHV 0.01395 0.45997 7.74908
28 3A6T 8OG 0.02652 0.40655 7.75194
29 1KTG AMP 0.03448 0.41068 8.69565
30 2IYL GDP 0.04369 0.40525 9.50704
31 3TDV GDP 0.03006 0.40086 10.3321
32 4A6D SAM 0.005968 0.42785 10.7011
33 2WJG GDP 0.04927 0.40595 12.234
34 5E95 GDP 0.01962 0.40984 12.3711
35 1GRN GDP 0.03013 0.40082 13.6126
36 2ZR9 DTP 0.02051 0.42265 16.2362
37 5FHD ADP ALF 0.01679 0.40708 21.7712
38 1LOB MMA 0.04388 0.4087 34.6154
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