Receptor
PDB id Resolution Class Description Source Keywords
1INI 1.82 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPREB IOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+ ESCHERICHIA COLI YGBP CYTIDYLYLTRANSFERASE DEOXYXYLULOSE-5-PHOSPHATE PATHWAISOPRENOID BIOSYNTHESIS CDPME MG TRANSFERASE
Ref.: STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRIT SYNTHETASE INVOLVED IN MEVALONATE- INDEPENDENT ISOP BIOSYNTHESIS. NAT.STRUCT.BIOL. V. 8 641 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDM A:1001;
Valid;
none;
submit data
521.308 C14 H25 N3 O14 P2 C[C@]...
MG A:1002;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1I52 1.5 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOB IOSYNTHESIS ESCHERICHIA COLI CYTIDYLYLTRANSFERASE DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXPISOPRENOID BIOSYNTHESYS MEP TRANSFERASE
Ref.: STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRIT SYNTHETASE INVOLVED IN MEVALONATE- INDEPENDENT ISOP BIOSYNTHESIS. NAT.STRUCT.BIOL. V. 8 641 2001
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 1I52 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 1INI - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 1I52 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 1INI - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1I52 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 1INI - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
3 2XWL - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
4 2XWM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 4NAL ic50 = 2.2 uM H70 C10 H4 Br3 Cl2 N O c1c(cc(c(c....
6 5MRO ic50 = 2 uM Q9P C12 H9 Cl N4 O c1ccc(cc1)....
7 5HS2 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: CDM; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 CDM 1 1
2 C2G 0.795181 0.933333
3 CDP 0.695122 0.894737
4 HF4 0.690476 0.894737
5 CTP 0.690476 0.894737
6 7XL 0.678161 0.921053
7 0RC 0.640449 0.897436
8 CAR 0.621951 0.881579
9 C5P 0.621951 0.881579
10 C 0.621951 0.881579
11 C5G 0.614583 0.896104
12 CDC 0.610526 0.833333
13 CXY 0.591837 0.896104
14 2TM 0.582418 0.909091
15 CDP MG 0.579545 0.868421
16 A7R 0.566038 0.860759
17 1AA 0.561905 0.839506
18 CDP RB0 0.539216 0.896104
19 PMT 0.535714 0.878049
20 91P 0.521739 0.793103
21 AR3 0.518519 0.813333
22 CTN 0.518519 0.813333
23 MCN 0.512821 0.764045
24 2AA 0.512821 0.70297
25 GPC 0.495868 0.764045
26 FN5 0.495726 0.876543
27 I5A 0.493976 0.753247
28 NCC 0.483333 0.922078
29 C3P 0.483146 0.868421
30 PCD 0.48 0.731183
31 FZQ 0.48 0.784091
32 CSF 0.479339 0.876543
33 CSQ 0.477064 0.860759
34 CSV 0.477064 0.860759
35 HQ5 0.461538 0.766667
36 C5P SIA 0.451613 0.897436
37 G C 0.447154 0.77907
38 DCP 0.44 0.858974
39 G G 6MZ C 0.439024 0.8
40 16B 0.43617 0.825
41 C2P 0.434783 0.881579
42 YSC 0.432432 0.736264
43 GTF 0.431373 0.8125
44 YYY 0.428571 0.858974
45 UTP 0.428571 0.842105
46 UDP 0.427083 0.842105
47 U5F 0.424242 0.842105
48 DKZ 0.417582 0.7125
49 GCQ 0.415842 0.8125
50 UPP 0.415094 0.820513
51 UDH 0.415094 0.85
52 CG2 0.404762 0.811765
53 5HM 0.402062 0.884615
54 UNP 0.401961 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: CDM; Similar ligands found: 1
No: Ligand Similarity coefficient
1 UAD 0.8607
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1I52; Ligand: CTP; 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: 1i52.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1I52; Ligand: CTP; 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: 1i52.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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