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 = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
6 2GZL Kd = 15 uM 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: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 C5P 1 1
2 CAR 1 1
3 C 1 1
4 CDP 0.787879 0.985507
5 HF4 0.753623 0.985507
6 CTP 0.753623 0.985507
7 2TM 0.732394 0.944444
8 0RC 0.689189 0.905405
9 7XL 0.689189 0.930556
10 16B 0.676471 0.930556
11 CTN 0.672131 0.842857
12 AR3 0.672131 0.842857
13 C2G 0.662338 0.943662
14 I5A 0.634921 0.828571
15 C5G 0.634146 0.930556
16 C C 0.632911 0.942857
17 C C C C 0.62963 0.929577
18 CDC 0.62963 0.8375
19 CDM 0.621951 0.881579
20 CXY 0.607143 0.930556
21 TKW 0.591549 0.985507
22 C3P 0.585714 0.956522
23 5HM 0.575342 0.944444
24 U 0.571429 0.941176
25 U5P 0.571429 0.941176
26 CSQ 0.555556 0.917808
27 CSV 0.555556 0.917808
28 1AA 0.554348 0.893333
29 C2P 0.541667 0.942857
30 PMT 0.540816 0.860759
31 DCM 0.540541 0.902778
32 DC 0.540541 0.902778
33 HQ5 0.523256 0.767442
34 DKZ 0.521127 0.733333
35 YSC 0.5 0.776471
36 91P 0.495146 0.839506
37 FN5 0.495146 0.858974
38 DOC 0.493333 0.902778
39 ICR 0.486842 0.861111
40 5BU 0.486842 0.876712
41 MCN 0.485714 0.807229
42 2AA 0.485714 0.683673
43 GPC 0.481481 0.829268
44 G C 0.481132 0.848101
45 5FU 0.48 0.876712
46 A C A C 0.477064 0.846154
47 CSF 0.476636 0.858974
48 PCD 0.464286 0.770115
49 U A C C 0.463636 0.857143
50 C5P SIA 0.458716 0.88
51 YYY 0.451219 0.890411
52 CNU 0.45 0.915493
53 UDP 0.45 0.927536
54 44P 0.448718 0.888889
55 DCP 0.447059 0.890411
56 G G G C 0.442478 0.860759
57 A G C C 0.438596 0.858974
58 GTF 0.436782 0.890411
59 V12 0.43617 0.7375
60 NUP 0.435897 0.929577
61 GCQ 0.435294 0.890411
62 UTP 0.433735 0.927536
63 A U C C 0.429752 0.846154
64 2KH 0.428571 0.901408
65 UP6 0.428571 0.887324
66 U5F 0.428571 0.927536
67 NVG 0.427083 0.719512
68 G C C C 0.423729 0.871795
69 S5P 0.423077 0.853333
70 GEO 0.418919 0.77027
71 H2U 0.415584 0.861111
72 UDP UDP 0.414634 0.898551
73 FNU 0.4125 0.88
74 JW5 0.4125 0.901408
75 8GM 0.411765 0.906667
76 DCZ 0.410959 0.77027
77 LDC 0.410959 0.77027
78 UPU 0.409091 0.9
79 BMP 0.405063 0.901408
80 BMQ 0.402597 0.885714
81 UNP 0.402299 0.901408
82 DCT 0.402299 0.890411
83 8OP 0.402299 0.853333
84 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2pmp.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
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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