Receptor
PDB id Resolution Class Description Source Keywords
1IV2 1.55 Å EC: 4.6.1.12 STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (BOUND FORM CDP) THERMUS THERMOPHILUS ISOPRENOID NON-MEVALONATE SYNTHASE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI STRUCTURAL GENOMICS LYASE
Ref.: STRUCTURE AND CATALYTIC MECHANISM OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE (MECDP) SYNTHASE, AN ENZYME IN THE NON-MEVALONATE PATHWAY OF ISOPRENOID SYNTHESIS. ACTA CRYSTALLOGR.,SECT.D V. 59 23 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDP A:1601;
B:1602;
B:1603;
D:1604;
E:1605;
E:1606;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
MG A:1561;
A:1571;
B:1562;
B:1572;
B:1573;
C:1563;
D:1564;
E:1565;
E:1575;
E:1576;
F:1566;
F:1574;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1IV2 1.55 Å EC: 4.6.1.12 STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE (BOUND FORM CDP) THERMUS THERMOPHILUS ISOPRENOID NON-MEVALONATE SYNTHASE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI STRUCTURAL GENOMICS LYASE
Ref.: STRUCTURE AND CATALYTIC MECHANISM OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE (MECDP) SYNTHASE, AN ENZYME IN THE NON-MEVALONATE PATHWAY OF ISOPRENOID SYNTHESIS. ACTA CRYSTALLOGR.,SECT.D V. 59 23 2003
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1IV2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1IV2 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
2 1IV4 - C5P C9 H14 N3 O8 P 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1IV2; Ligand: CDP; Similar sites found: 11
This union binding pocket(no: 1) in the query (biounit: 1iv2.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5GT9 NAP 0.01715 0.40902 1.97368
2 1WRA PC 0.008939 0.42421 3.28947
3 3NUG NAD 0.02323 0.40259 3.94737
4 4OHB 5HM 0.007105 0.41288 6.57895
5 4JK3 NAD 0.02036 0.40297 7.89474
6 3KIH GDL 0.009069 0.41699 8.24742
7 4ISS TAR 0.008289 0.42325 8.55263
8 4N9Z V3L 0.03922 0.40483 9.86842
9 2GCG DGY 0.03268 0.40009 11.1842
10 5KMS FAD 0.02938 0.40289 13.1579
11 5C2N NAG 0.01788 0.40397 16.6667
12 1W55 C 0.000005538 0.52332 50
Pocket No.: 2; Query (leader) PDB : 1IV2; 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: 1iv2.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1IV2; Ligand: CDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1iv2.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1IV2; Ligand: CDP; Similar sites found: 1
This union binding pocket(no: 4) in the query (biounit: 1iv2.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1AE1 NAP 0.01804 0.41024 5.26316
Pocket No.: 5; Query (leader) PDB : 1IV2; Ligand: CDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1iv2.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1IV2; Ligand: CDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1iv2.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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