Receptor
PDB id Resolution Class Description Source Keywords
5B6D 1.65 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF CYTIDINE MONOPHOSPHATE HYDROXYMETHYLASE CMP STREPTOMYCES RIMOFACIENS CMP HYDROXYMETHYLASE TRANSFERASE
Ref.: STRUCTURAL BASIS OF THE SUBSTRATE PREFERENCE TOWARD A THYMIDYLATE SYNTHASE MILA INVOLVED IN MILDIOMYCIN BIOSYNTHESIS SCI REP V. 6 39675 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C5P B:401;
A:401;
Valid;
Valid;
none;
none;
submit data
323.197 C9 H14 N3 O8 P C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5B6D 1.65 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF CYTIDINE MONOPHOSPHATE HYDROXYMETHYLASE CMP STREPTOMYCES RIMOFACIENS CMP HYDROXYMETHYLASE TRANSFERASE
Ref.: STRUCTURAL BASIS OF THE SUBSTRATE PREFERENCE TOWARD A THYMIDYLATE SYNTHASE MILA INVOLVED IN MILDIOMYCIN BIOSYNTHESIS SCI REP V. 6 39675 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5B6D - C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 5JP9 - DCM C9 H14 N3 O7 P C1[C@@H]([....
3 5B6E - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5B6D - C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 5JP9 - DCM C9 H14 N3 O7 P C1[C@@H]([....
3 5B6E - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5B6D - C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 5JP9 - DCM C9 H14 N3 O7 P C1[C@@H]([....
3 5B6E - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
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 : 5B6D; Ligand: C5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5b6d.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5B6D; Ligand: C5P; Similar sites found: 25
This union binding pocket(no: 2) in the query (biounit: 5b6d.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DLG GWE 0.04597 0.40668 2.76923
2 3NRR UMP 0.000001001 0.59982 16
3 1I00 D16 0.000000805 0.60203 17.2414
4 1I00 UMP 0.000000805 0.60203 17.2414
5 4EIL UMP 0.00000006892 0.61479 17.5385
6 1J3I UMP 0.00000005786 0.65735 18.7692
7 1F28 UMP 0.00000005764 0.61843 19.8653
8 2AAZ UMP 0.0000001076 0.60721 21.1356
9 1B5E DCM 0.00003594 0.52898 27.6423
10 1NCE UMP 0.00000002767 0.62137 28.4091
11 1SYN UMP 0.00000002088 0.6244 28.6792
12 1AXW UMP 0.00000004274 0.61266 28.6792
13 1TSD UMP 0.00000002319 0.61112 28.6792
14 1TLC DGP 0.0000001552 0.59 28.6792
15 1DDU DDU 0.0000002727 0.55541 28.6792
16 1TDU DUR 0.0000003819 0.55076 28.6792
17 4ISK UMP 0.00000003556 0.6033 28.7879
18 1ZPR UMP 0.00000004352 0.6 28.7879
19 1AIQ UMP 0.0000001077 0.58617 28.7879
20 2KCE D16 0.000005862 0.58537 28.7879
21 2A9W UMP 0.0000000324 0.56285 28.7879
22 1JG0 UMP 0.00000009173 0.54293 28.7879
23 1F4G TP4 0.0004037 0.46286 28.7879
24 5H3A D16 0.0000003753 0.59568 33.5689
25 5H3A UMP 0.00000005068 0.59568 33.5689
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