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Receptor
PDB id Resolution Class Description Source Keywords
2PMP 2.3 Å EC: 4.6.1.12 STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYN THE ISOPRENOID BIOSYNTHETIC PATHWAY OF ARABIDOPSIS THALIANA ARABIDOPSIS THALIANA PLANT ENZYMES ARABIDOPSIS THALIANA MEP PATHWAY ISOPRENOIDPROTEINS CMP ZINC IONS LYASE
Ref.: BIOSYNTHESIS OF ISOPRENOIDS IN PLANTS: STRUCTURE OF 2C-METHYL-D-ERITHRYTOL 2,4-CYCLODIPHOSPHATE SYNTHAS ARABIDOPSIS THALIANA. COMPARISON WITH THE BACTERIAL PROTEIN SCI. V. 16 2082 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C5P A:700;
Valid;
none;
submit data
323.197 C9 H14 N3 O8 P C1=CN...
CL A:702;
Invalid;
none;
submit data
35.453 Cl [Cl-]
PO4 A:701;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
ZN A:500;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PMP 2.3 Å EC: 4.6.1.12 STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYN THE ISOPRENOID BIOSYNTHETIC PATHWAY OF ARABIDOPSIS THALIANA ARABIDOPSIS THALIANA PLANT ENZYMES ARABIDOPSIS THALIANA MEP PATHWAY ISOPRENOIDPROTEINS CMP ZINC IONS LYASE
Ref.: BIOSYNTHESIS OF ISOPRENOIDS IN PLANTS: STRUCTURE OF 2C-METHYL-D-ERITHRYTOL 2,4-CYCLODIPHOSPHATE SYNTHAS ARABIDOPSIS THALIANA. COMPARISON WITH THE BACTERIAL PROTEIN SCI. V. 16 2082 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 2PMP - C5P C9 H14 N3 O8 P 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 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
15 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
16 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
17 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
18 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
19 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
20 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
21 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
22 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
23 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
24 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
25 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
26 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
27 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
28 2UZH - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C5P; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 C5P 1 1
2 C 1 1
3 CAR 1 1
4 CDP 0.787879 0.985507
5 HF4 0.753623 0.985507
6 CTP 0.753623 0.985507
7 7XL 0.689189 0.930556
8 16B 0.676471 0.930556
9 AR3 0.672131 0.842857
10 CTN 0.672131 0.842857
11 C2G 0.662338 0.943662
12 I5A 0.634921 0.828571
13 C5G 0.634146 0.930556
14 C C 0.632911 0.942857
15 C C C C 0.62963 0.929577
16 CDC 0.62963 0.8375
17 CDM 0.621951 0.881579
18 CXY 0.607143 0.930556
19 TKW 0.591549 0.985507
20 C3P 0.585714 0.956522
21 5HM 0.575342 0.944444
22 U 0.571429 0.941176
23 U5P 0.571429 0.941176
24 CSV 0.555556 0.917808
25 CSQ 0.555556 0.917808
26 1AA 0.554348 0.893333
27 C2P 0.541667 0.942857
28 PMT 0.540816 0.860759
29 DCM 0.540541 0.902778
30 DC 0.540541 0.902778
31 DKZ 0.521127 0.733333
32 FN5 0.495146 0.858974
33 91P 0.495146 0.839506
34 DOC 0.493333 0.902778
35 ICR 0.486842 0.861111
36 5BU 0.486842 0.876712
37 2AA 0.485714 0.683673
38 MCN 0.485714 0.807229
39 GPC 0.481481 0.829268
40 G C 0.481132 0.848101
41 5FU 0.48 0.876712
42 A C A C 0.477064 0.846154
43 CSF 0.476636 0.858974
44 PCD 0.464286 0.770115
45 U A C C 0.463636 0.857143
46 C5P SIA 0.458716 0.88
47 YYY 0.451219 0.890411
48 CNU 0.45 0.915493
49 UDP 0.45 0.927536
50 44P 0.448718 0.888889
51 DCP 0.447059 0.890411
52 G G G C 0.442478 0.860759
53 A G C C 0.438596 0.858974
54 GTF 0.436782 0.890411
55 V12 0.43617 0.7375
56 NUP 0.435897 0.929577
57 GCQ 0.435294 0.890411
58 UTP 0.433735 0.927536
59 A U C C 0.429752 0.846154
60 2KH 0.428571 0.901408
61 UP6 0.428571 0.887324
62 NVG 0.427083 0.719512
63 G C C C 0.423729 0.871795
64 S5P 0.423077 0.853333
65 GEO 0.418919 0.77027
66 H2U 0.415584 0.861111
67 UDP UDP 0.414634 0.898551
68 FNU 0.4125 0.88
69 JW5 0.4125 0.901408
70 8GM 0.411765 0.906667
71 DCZ 0.410959 0.77027
72 LDC 0.410959 0.77027
73 UPU 0.409091 0.9
74 BMP 0.405063 0.901408
75 BMQ 0.402597 0.885714
76 8OP 0.402299 0.853333
77 UNP 0.402299 0.901408
78 U6M 0.4 0.914286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PMP; Ligand: C5P; Similar sites found with APoc: 12
This union binding pocket(no: 1) in the query (biounit: 2pmp.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1S4M LUM 4.375
2 2VJM COA 5
3 1DKU AP2 5
4 2BME GNP 6.25
5 3GJX GTP 6.875
6 5CGE 51F 6.875
7 3A06 NDP 8.125
8 1WA5 GTP 15.625
9 5UWI GNP 20.625
10 6CIT GNP 20.625
11 3WYF GTP 20.625
12 5UWQ GNP 20.625
Pocket No.: 2; Query (leader) PDB : 2PMP; Ligand: C5P; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2pmp.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2PMP; Ligand: C5P; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2pmp.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
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