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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;
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
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 253 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 209 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 173 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: 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 : 4JEM; Ligand: C5P; Similar sites found with APoc: 100
This union binding pocket(no: 1) in the query (biounit: 4jem.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZRU FMN None
2 5NGZ 2BG None
3 3KIH GDL None
4 3ZZS TRP None
5 2XRH NIO None
6 2E1A MSE None
7 1U9L ASN ARG PRO ILE LEU SER LEU None
8 1Q6O LG6 None
9 5ZI9 FLC 1.76471
10 5GOO FRU 1.76471
11 1H8P PC 1.83486
12 2OI2 DP6 2.35294
13 4EKQ NPO 2.35294
14 3ROE THM 2.35294
15 3WUR O4B 2.92398
16 2FN1 SAL 2.94118
17 1LYX PGA 2.94118
18 3VC3 C6P 2.94118
19 1Q9I TEO 2.94118
20 1Q9I FAD 2.94118
21 2WQ4 SFU 3.20513
22 5ZBL AMP 3.52941
23 5KY4 GDP 3.52941
24 5KY5 GDP 3.52941
25 2VN9 GVD 3.52941
26 1YRO UDP 3.52941
27 5KXQ GDP 3.52941
28 5KY9 GDP 3.52941
29 4M5P FMN 3.52941
30 4K7O EKZ 3.57143
31 3KIF GDL 3.77358
32 3WIR BGC 4.11765
33 2BES RES 4.11765
34 3IX1 NFM 4.11765
35 4KVL PLM 4.11765
36 3ZZQ TRP 4.61538
37 2CFC KPC 4.70588
38 1GPM CIT 4.70588
39 5DQY BEZ 4.7619
40 2Q2Y MKR 5.29412
41 2Q2Y ADP 5.29412
42 2IMP LAC 5.29412
43 3IP8 B85 5.29412
44 5NM7 GLY 5.6391
45 4DE3 DN8 5.88235
46 2FAH MLA 5.88235
47 3EXS 5RP 5.88235
48 4FMS BDP 5.88235
49 3U1T MLI 5.88235
50 2CHT TSA 6.29921
51 4WBD CIT 6.47059
52 5A1S FLC 6.47059
53 2B4B COA 6.47059
54 4A01 2PN 6.47059
55 5ZA2 NXL 6.47059
56 3C3N FMN 6.47059
57 1IV2 CDP 6.57895
58 6A56 LAT 6.70732
59 5LXT GDP 7.05882
60 4TVD BGC 7.05882
61 4HE2 AMP 7.05882
62 4N02 FNR 7.05882
63 1S2D ADE 7.18563
64 5K8P 6R8 7.64706
65 5CSS G3P 7.64706
66 4M3P HCS 7.64706
67 1NXJ TLA 8.19672
68 5EYY MDM 8.23529
69 2GNM MAN 8.82353
70 2PHX MAN MAN 8.82353
71 1Q8Q MAN MMA 8.82353
72 1Q8S MAN MMA 8.82353
73 5W6Y TRP 8.82353
74 1Q8V MAN MAN MAN 8.82353
75 2VCN ISZ 8.82353
76 2PHX MAN MAN MAN MAN 8.82353
77 5AJU RP5 9.41177
78 2F2U M77 9.41177
79 4RJK TPP 9.41177
80 5GQI CTP 10.5882
81 1JT1 MCO 10.5882
82 1GVF PGH 10.5882
83 1F8Y 5MD 10.828
84 4FHT DHB 10.828
85 5E9H MLI 11.7647
86 2CI5 HCS 11.7647
87 1A99 PUT 11.7647
88 3ZEI AWH 11.7647
89 2WDQ CBE 12.3529
90 5UI2 SUC 12.3529
91 3QH2 3NM 13.5294
92 4KXL 6C6 13.8158
93 2JK0 ASP 14.1176
94 2J5B TYE 14.7059
95 1F6D UDP 14.7059
96 1CT9 GLN 14.7059
97 5ENZ UDP 15.2941
98 5WGG SAM 17.0588
99 4G86 BNT 18.2353
100 4P5E N6P 23.6842
Pocket No.: 2; Query (leader) PDB : 4JEM; Ligand: C5P; Similar sites found with APoc: 45
This union binding pocket(no: 2) in the query (biounit: 4jem.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2F2T 5IQ None
2 1HBK MYR None
3 1FWV SGA MAG FUC None
4 5GOP FRU 1.76471
5 4B5W PYR 2.94118
6 5J60 FAD 2.94118
7 4UP5 94W 3.52941
8 5C9P FUC 3.52941
9 3VSS FRU 4.11765
10 2RAB FAD 4.11765
11 6CI9 F3V 4.11765
12 4NTO 1PW 4.70588
13 3A1I UNU 5.29412
14 2YPI PGA 5.29412
15 2R5N TPP 5.29412
16 2R5N RP5 5.29412
17 1D6S MET PLP 5.88235
18 4PTN PYR 5.88235
19 1D6S PLP MET 5.88235
20 1W6F ISZ 6.47059
21 6CS8 F9Y 6.47059
22 6HKE MLT 6.47059
23 1FEC FAD 7.05882
24 1OFD FMN 8.23529
25 1W0O SIA 8.23529
26 1LDN NAD 8.23529
27 1OFD AKG 8.23529
28 2PHU MAN MAN 8.82353
29 1Q8O MAN MMA 8.82353
30 1Q8P MAN MMA 8.82353
31 2PHW MAN MAN 8.82353
32 2PHR MAN MAN BMA MAN 8.82353
33 2GND MAN MMA 8.82353
34 2PHR MAN MAN 8.82353
35 4JEJ 1GP 9.41177
36 1LNX URI 9.87654
37 4ZUL UN1 10.5882
38 4YJK URA 11.1765
39 5L2R MLA 11.1765
40 3BEO UDP 12.3529
41 2JFZ DGL 12.9412
42 2JFZ 003 12.9412
43 2HQM FAD 14.7059
44 5YJS SAL 17.0588
45 1MO9 KPC 21.1765
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