Receptor
PDB id Resolution Class Description Source Keywords
4JEM 1.55 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF MILB COMPLEXED WITH CYTIDINE 5'-MONOPHO STREPTOMYCES RIMOFACIENS CMP N-GLYCOSIDASE HYDROLASE
Ref.: REVERSAL OF THE SUBSTRATE SPECIFICITY OF CMP N-GLYC TO DCMP. BIOCHEMISTRY V. 52 4037 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C5P A:201;
B:201;
Valid;
Valid;
none;
none;
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323.197 C9 H14 N3 O8 P C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JEM 1.55 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF MILB COMPLEXED WITH CYTIDINE 5'-MONOPHO STREPTOMYCES RIMOFACIENS CMP N-GLYCOSIDASE HYDROLASE
Ref.: REVERSAL OF THE SUBSTRATE SPECIFICITY OF CMP N-GLYC TO DCMP. BIOCHEMISTRY V. 52 4037 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4JEM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 4OHB - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
2 4JEM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 4OHB - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
2 4JEM - C5P C9 H14 N3 O8 P 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 : 4JEM; Ligand: C5P; Similar sites found: 42
This union binding pocket(no: 1) in the query (biounit: 4jem.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5XVQ 8GC 0.0107 0.42312 None
2 2XRH NIO 0.01792 0.40729 None
3 1U9L ASN ARG PRO ILE LEU SER LEU 0.01846 0.40288 None
4 2E1A MSE 0.02182 0.4011 None
5 1SW0 PGA 0.01276 0.40456 2.35294
6 2FN1 SAL 0.01208 0.41395 2.94118
7 3VC3 C6P 0.006884 0.40726 2.94118
8 1Q9I TEO 0.03839 0.40063 2.94118
9 5KY5 GDP 0.008188 0.41372 3.52941
10 2VN9 GVD 0.01664 0.40699 3.52941
11 1YRO UDP 0.02829 0.40664 3.52941
12 4M5P FMN 0.004128 0.40334 3.52941
13 4K7O EKZ 0.04163 0.40024 3.57143
14 3WIR BGC 0.0189 0.41065 4.11765
15 2BES RES 0.01243 0.4051 4.11765
16 3IX1 NFM 0.02374 0.40342 4.11765
17 2CFC KPC 0.02509 0.40333 4.70588
18 1GPM CIT 0.02664 0.40282 4.70588
19 2Q2Y ADP 0.02503 0.41838 5.29412
20 2Q2Y MKR 0.02503 0.41838 5.29412
21 2IMP LAC 0.01338 0.41581 5.29412
22 3IP8 B85 0.01048 0.41271 5.29412
23 2FAH MLA 0.007233 0.43249 5.88235
24 3EXS 5RP 0.00642 0.42306 5.88235
25 4FMS BDP 0.02513 0.40214 5.88235
26 4A01 2PN 0.02148 0.40144 6.47059
27 4N02 FNR 0.007286 0.40468 7.05882
28 1S2D ADE 0.0003305 0.43125 7.18563
29 2GNM MAN 0.01331 0.41788 8.82353
30 1Q8Q MAN MMA 0.01678 0.41311 8.82353
31 1Q8S MAN MMA 0.01792 0.41168 8.82353
32 2F2U M77 0.01043 0.41281 9.41177
33 1JT1 MCO 0.03093 0.40279 10.5882
34 1GVF PGH 0.02559 0.40173 10.5882
35 4FHT DHB 0.0289 0.40156 10.828
36 2CI5 HCS 0.01584 0.41305 11.7647
37 1A99 PUT 0.0244 0.40394 11.7647
38 3ZEI AWH 0.011 0.40248 11.7647
39 2WDQ CBE 0.008915 0.42776 12.3529
40 2J5B TYE 0.01416 0.42388 14.7059
41 1F6D UDP 0.01278 0.4085 14.7059
42 4P5E N6P 0.000001964 0.53421 23.6842
Pocket No.: 2; Query (leader) PDB : 4JEM; Ligand: C5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4jem.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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