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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 293 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 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....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 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: 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 : 5B6D; Ligand: C5P; Similar sites found with APoc: 42
This union binding pocket(no: 1) in the query (biounit: 5b6d.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 6BU0 IHP None
2 3WH2 FLC 1.36054
3 1PZM 5GP 1.4218
4 4UXU MLK 1.83486
5 5G6U YJM 1.91571
6 5WJ6 B4A 3.38462
7 3VOZ 04A 3.49206
8 4WQQ MAN 3.5461
9 1QHO MAL 3.69231
10 3P7G MAN 4.79452
11 3HRD FAD 7.69231
12 2XQ0 BES 8
13 2CXG GLC GLC 8.30769
14 1TLG GAL 10.4
15 2G86 UMP 15.1899
16 3NRR D16 16
17 3NRR UMP 16
18 1I00 D16 17.2414
19 1I00 UMP 17.2414
20 4EIL UMP 17.5385
21 1J3I UMP 18.7692
22 1F28 UMP 19.8653
23 2AAZ UMP 21.1356
24 1B5E DCM 27.6423
25 1NCE UMP 28.4091
26 1SYN UMP 28.6792
27 1TSD UMP 28.6792
28 1AXW UMP 28.6792
29 1TDU DUR 28.6792
30 1TLC DGP 28.6792
31 1DDU DDU 28.6792
32 4ISK UMP 28.7879
33 1ZPR UMP 28.7879
34 1AIQ UMP 28.7879
35 2A9W UMP 28.7879
36 2KCE D16 28.7879
37 1JG0 UMP 28.7879
38 1F4G TP4 28.7879
39 6CDZ UMC 28.8973
40 6CDZ UMP 28.8973
41 5H3A D16 33.5689
42 5H3A UMP 33.5689
Pocket No.: 2; Query (leader) PDB : 5B6D; Ligand: C5P; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 5b6d.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2O66 FLC 2.22222
2 5K0A FAD 4.61538
3 4B5W PYR 6.64062
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