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 (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: C5P; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 C 1 1
2 CAR 1 1
3 C5P 1 1
4 CDP 0.787879 0.985507
5 CTP 0.753623 0.985507
6 CDP MG 0.724638 0.916667
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 CDC 0.62963 0.8375
16 CDM 0.621951 0.881579
17 CXY 0.607143 0.930556
18 TKW 0.591549 0.985507
19 C3P 0.585714 0.956522
20 5HM 0.575342 0.944444
21 U5P 0.571429 0.941176
22 CSV 0.555556 0.917808
23 CSQ 0.555556 0.917808
24 1AA 0.554348 0.893333
25 C2P 0.541667 0.942857
26 PMT 0.540816 0.860759
27 DCM 0.540541 0.902778
28 DC 0.540541 0.902778
29 DKZ 0.521127 0.733333
30 91P 0.495146 0.839506
31 FN5 0.495146 0.858974
32 DOC 0.493333 0.902778
33 ICR 0.486842 0.861111
34 5BU 0.486842 0.876712
35 2AA 0.485714 0.683673
36 MCN 0.485714 0.807229
37 GPC 0.481481 0.829268
38 G C 0.481132 0.848101
39 5FU 0.48 0.876712
40 CSF 0.476636 0.858974
41 PCD 0.464286 0.770115
42 U A C C 0.463636 0.857143
43 C5P SIA 0.458716 0.88
44 YYY 0.451219 0.890411
45 CNU 0.45 0.915493
46 UDP 0.45 0.927536
47 44P 0.448718 0.888889
48 DCP 0.447059 0.890411
49 G G G C 0.442478 0.860759
50 A G C C 0.438596 0.858974
51 V12 0.43617 0.7375
52 NUP 0.435897 0.929577
53 GCQ 0.435294 0.890411
54 UTP 0.433735 0.927536
55 A U C C 0.429752 0.846154
56 2KH 0.428571 0.901408
57 UP6 0.428571 0.887324
58 NVG 0.427083 0.719512
59 G C C C 0.423729 0.871795
60 S5P 0.423077 0.853333
61 GEO 0.418919 0.77027
62 CH 0.417722 0.956522
63 H2U 0.415584 0.861111
64 UDP UDP 0.414634 0.898551
65 FNU 0.4125 0.88
66 JW5 0.4125 0.901408
67 8GM 0.411765 0.906667
68 DCZ 0.410959 0.77027
69 LDC 0.410959 0.77027
70 UPU 0.409091 0.9
71 BMP 0.405063 0.901408
72 BMQ 0.402597 0.885714
73 UNP 0.402299 0.901408
74 8OP 0.402299 0.853333
75 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: 119
This union binding pocket(no: 1) in the query (biounit: 2pmp.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F81 STT 0.0001899 0.50948 None
2 3H86 AP5 0.00007978 0.50158 None
3 1NU4 MLA 0.001338 0.48919 None
4 2D4N DUP 0.0002938 0.44948 None
5 1WGC SIA GAL BGC 0.006762 0.44175 None
6 2WGC SIA GAL BGC 0.01241 0.43696 None
7 1H8G CHT 0.02278 0.42262 None
8 3S9K CIT 0.0394 0.41941 None
9 2GJ3 FAD 0.03334 0.40948 None
10 1UO5 PIH 0.03974 0.4094 None
11 1UO4 PIH 0.0297 0.40853 None
12 3R51 MMA 0.02809 0.40286 None
13 1M5B BN1 0.02946 0.40269 None
14 4LTN NAI 0.00008435 0.50221 1.875
15 1W3R PYR 0.000208 0.49699 1.875
16 4LTN FMN 0.00381 0.43031 1.875
17 3EJ0 11X 0.003544 0.4162 1.875
18 4N02 FNR 0.02408 0.40369 1.875
19 4F8L GAL 0.003645 0.46571 2.06897
20 2IMP NAI 0.003829 0.45185 2.5
21 4JCA CIT 0.005919 0.44472 2.5
22 1FBL HTA 0.001227 0.4207 2.5
23 3GD8 GOL 0.002957 0.41258 2.5
24 2IMP LAC 0.00257 0.40776 2.5
25 3BY8 MLT 0.00817 0.41544 2.8169
26 1DUC DUD 0.003284 0.40478 2.98507
27 2BZ1 TAU 0.00228 0.4767 3.125
28 3FSJ D7K 0.004247 0.44515 3.125
29 3VCA PRO 0.002563 0.42201 3.125
30 2BGM NAJ 0.02421 0.40633 3.125
31 2O66 FLC 0.00141 0.43588 3.7037
32 1JN2 SFP 0.01084 0.46626 3.75
33 2ZWS PLM 0.005099 0.45784 3.75
34 4TSK NDP 0.001495 0.45748 3.75
35 4M6T SAM 0.00144 0.44223 3.75
36 4M5P MLA 0.02086 0.4165 3.75
37 4W6Z ETF 0.01741 0.41315 3.75
38 1DXY COI 0.01773 0.41276 3.75
39 3O03 NAP 0.02291 0.40735 3.75
40 4B9E FAH 0.01558 0.40271 3.75
41 1B66 BIO 0.002064 0.41502 4.28571
42 1MVN PCO 0.002484 0.44781 4.375
43 2X61 NGA GAL SIA 0.006671 0.43008 4.375
44 4AAW R84 0.00477 0.4299 4.375
45 1S4M LUM 0.01284 0.42935 4.375
46 1MVN FMN 0.003177 0.42846 4.375
47 4CMF PXG 0.01567 0.41006 4.375
48 2A0W DIH 0.008105 0.40726 4.375
49 1Y1A GSH 0.04895 0.40707 4.375
50 1SS4 GSH 0.004593 0.46373 4.57516
51 4RJK PYR 0.001026 0.4954 5
52 2BNE U5P 0.0006255 0.45108 5
53 4COQ SAN 0.002357 0.43291 5
54 2NZ2 ASP 0.002096 0.42267 5
55 4M7F BM3 0.002424 0.42011 5
56 1OTH PAO 0.003925 0.41783 5
57 3RO7 TDR 0.03977 0.41284 5
58 3FPZ AHZ 0.04277 0.40565 5
59 3A8U PLP 0.005628 0.40201 5
60 3NOJ PYR 0.0004519 0.45305 5.46218
61 3QDY CBS 0.009372 0.41274 5.59441
62 3QDY A2G GAL 0.01341 0.41188 5.59441
63 3FS8 TDR 0.0002888 0.49761 5.625
64 3FS8 ACO 0.003302 0.45688 5.625
65 4OYA 1VE 0.009015 0.44327 5.625
66 2YIV YIV 0.005814 0.42901 5.625
67 1Y7P RIP 0.009257 0.41949 5.625
68 3I8T LBT 0.002874 0.41712 5.625
69 1F8F NAD 0.01611 0.41248 5.625
70 1OWB NAD 0.008539 0.40276 5.625
71 1BTN I3P 0.002527 0.47482 5.66038
72 4DN8 BMA 0.00008714 0.49513 5.76923
73 2PNZ UDP 0.002451 0.41726 5.77617
74 2XBP ATP 0.01275 0.41099 6.19469
75 1D09 PAL 0.001005 0.48899 6.25
76 1X1T NAD 0.001167 0.47068 6.25
77 2BLE 5GP 0.01381 0.41805 6.25
78 4N69 SER 0.005488 0.40837 6.25
79 2BME GNP 0.03224 0.40684 6.25
80 2C7G FAD 0.03016 0.4016 6.25
81 2C7G ODP 0.02908 0.4016 6.25
82 2HVK TBA 0.00009312 0.49388 6.45161
83 1EXB NDP 0.01009 0.43008 6.875
84 1SBZ FMN 0.004178 0.41677 6.875
85 1ZED PNP 0.007691 0.41663 6.875
86 1EDO NAP 0.0194 0.41659 6.875
87 2C31 TZD 0.03898 0.40495 6.875
88 3GJX GTP 0.03557 0.40453 6.875
89 1JA9 NDP 0.0005503 0.48341 7.5
90 1RY2 AMP 0.002164 0.41932 7.5
91 1WVC CTP 0.04471 0.40665 7.5
92 4LO6 SIA GAL 0.0006168 0.47037 8.125
93 1OFH ADP 0.004639 0.40674 8.125
94 4KCF AKM 0.01955 0.40603 8.125
95 3B9Z CO2 0.000002566 0.56163 8.75
96 3K3G MMU 0.00002151 0.50747 8.75
97 3BRE C2E 0.003197 0.42715 8.75
98 1I0Z OXM 0.0151 0.4162 8.75
99 2YYJ 4HP 0.001227 0.47468 9.375
100 2YYJ FAD 0.001227 0.47468 9.375
101 1GPJ CIT 0.0003476 0.46903 9.375
102 3VKX T3 0.003815 0.40238 9.375
103 1DL7 NCH 0.005304 0.45692 9.82143
104 1XMV ADP 0.02611 0.40149 10
105 3MB5 SAM 0.006497 0.42599 10.625
106 1NME 159 0.001788 0.40482 11.6438
107 1RZM E4P 0.01201 0.40786 12.5
108 1NXJ GLV 0.00002201 0.49452 13.125
109 3TA2 AKG 0.003428 0.41614 13.5593
110 3TA2 ATP 0.01094 0.40211 13.5593
111 1GSA GSH 0.004266 0.42638 15
112 4G1V FAD 0.01635 0.43031 15.625
113 1WA5 GTP 0.04497 0.40396 15.625
114 4JLV ADP 0.04887 0.40072 15.625
115 1SC3 MLI 0.0006974 0.47231 15.9091
116 4Q3F TLA 0.0007587 0.4543 18.8034
117 1Q3Q ANP 0.01549 0.41458 20.625
118 3WYF GTP 0.04504 0.40108 20.625
119 2VKL MLT 0.005246 0.44742 25.5556
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