Receptor
PDB id Resolution Class Description Source Keywords
2UZH 2.2 Å EC: 4.6.1.12 MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4- CYCLODIPHOSPHATE SYNTHASE (ISPF) MYCOBACTERIUM SMEGMATIS ISPF LYASE MYCOBACTERIA COMPLEX WITH CDP NON-MEVALONATE PATHWAY OF ISOPRENOID BIOSYNTHESIS
Ref.: THE STRUCTURE OF MYCOBACTERIA 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE, AN ESSENTIAL ENZYME, PROVIDES A PLATFORM FOR DRUG DISCOVERY. BMC STRUCT.BIOL. V. 7 68 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT C:1162;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
CDP A:1158;
B:1158;
C:1158;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
EDO A:1160;
C:1160;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GOL A:1161;
B:1161;
C:1161;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
IPE B:1160;
Valid;
none;
submit data
246.092 C5 H12 O7 P2 CC(=C...
PEG B:1162;
B:1163;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
ZN A:1157;
B:1157;
C:1157;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2UZH 2.2 Å EC: 4.6.1.12 MYCOBACTERIUM SMEGMATIS 2C-METHYL-D-ERYTHRITOL-2,4- CYCLODIPHOSPHATE SYNTHASE (ISPF) MYCOBACTERIUM SMEGMATIS ISPF LYASE MYCOBACTERIA COMPLEX WITH CDP NON-MEVALONATE PATHWAY OF ISOPRENOID BIOSYNTHESIS
Ref.: THE STRUCTURE OF MYCOBACTERIA 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE, AN ESSENTIAL ENZYME, PROVIDES A PLATFORM FOR DRUG DISCOVERY. BMC STRUCT.BIOL. V. 7 68 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2UZH - 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 6 families.
1 2UZH - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
50% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8I - CIT C6 H8 O7 C(C(=O)O)C....
3 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 3ERN Kd ~ 40 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
6 2GZL ic50 = 3 mM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
7 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
8 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
9 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
11 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
12 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
13 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
14 4C81 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
15 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
16 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
17 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
18 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
19 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
20 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
21 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
22 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
23 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
24 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
25 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
26 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
27 1IV2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
28 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
29 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
30 2UZH - 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
Ligand no: 2; Ligand: IPE; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 IPE 1 1
2 IP8 0.617647 0.918919
3 0O3 0.589744 0.871795
4 0CJ 0.536585 0.780488
5 P23 0.527778 0.815789
6 ISY 0.487805 0.85
7 DED 0.487179 0.653061
8 IPR 0.475 0.820513
9 P25 0.463415 0.825
10 P22 0.444444 0.710526
11 0CH 0.439024 0.731707
12 43W 0.439024 0.789474
13 EIP 0.431818 0.846154
14 DMA 0.428571 0.794872
15 0JX 0.428571 0.810811
16 0K2 0.418605 0.74359
17 BHI 0.413043 0.767442
18 DP6 0.408163 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2UZH; 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: 2uzh.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2UZH; Ligand: CDP; 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: 2uzh.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2UZH; Ligand: CDP; Similar sites found: 14
This union binding pocket(no: 3) in the query (biounit: 2uzh.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UEC ALA ARG TPO LYS 0.02255 0.40938 None
2 3CM2 X23 0.0227 0.40265 None
3 2ZL4 ALA ALA ALA ALA 0.02619 0.40005 2.42424
4 1N4W FAD 0.03046 0.40228 3.0303
5 4RF7 ARG 0.02396 0.40566 4.24242
6 4MDB RLT 0.01901 0.40424 4.84848
7 4ISS TAR 0.01415 0.413 5.45455
8 1OCU PIB 0.02276 0.40934 5.55556
9 4N9Z V3L 0.03394 0.41764 6.06061
10 4U60 SIA GAL NGA 0.01969 0.40406 6.66667
11 1NC2 DOE 0.02392 0.40073 10.303
12 1DNP MHF 0.03474 0.40242 12.1212
13 5F7J ADE 0.02457 0.40092 18.1818
14 1W55 C 0.0007478 0.41751 49.0909
Pocket No.: 4; Query (leader) PDB : 2UZH; Ligand: IPE; Similar sites found: 23
This union binding pocket(no: 4) in the query (biounit: 2uzh.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QZR ANP 0.006526 0.44301 None
2 2FAV APR 0.03312 0.40579 None
3 4M7V NAP 0.04251 0.40527 None
4 3ZOK NAD 0.02548 0.41844 2.42424
5 5KZD RCJ 0.01113 0.41657 3.0303
6 3N0S ACO 0.03994 0.41088 3.0303
7 1RSG FAD 0.04035 0.41695 3.63636
8 3Q9T FAY 0.03321 0.41661 3.63636
9 4OR7 NAP 0.02343 0.41587 4.24242
10 4USR FAD 0.03707 0.41086 4.84848
11 3UOY NAP 0.03778 0.43221 5.45455
12 1DFO PLG 0.006291 0.43606 6.06061
13 1B7H LYS NLE LYS 0.01742 0.42885 6.06061
14 1YRO UDP 0.01373 0.40537 6.50407
15 2C42 PYR 0.02916 0.41365 7.27273
16 2MBR EPU 0.02547 0.43496 7.87879
17 2MBR FAD 0.02616 0.43496 7.87879
18 3AD8 NAD 0.04873 0.40524 9.09091
19 3WCA FPS 0.04359 0.40064 9.69697
20 2RHO GSP 0.03273 0.40283 11.5152
21 3CTY FAD 0.04381 0.41639 15.1515
22 2WSB NAD 0.02898 0.42342 27.2727
23 1W55 GPP 0.00001159 0.40716 49.0909
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