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Receptor
PDB id Resolution Class Description Source Keywords
4OHB 2.4 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF MILB E103A IN COMPLEX WITH 5- HYDROXYMETHYLCYTIDINE 5'-MONOPHOSPHATE (HMCMP) FROM STREPTOR IMOFACIENS STREPTOMYCES RIMOFACIENS HYDROLASE PROTEIN-HMCMP COMPLEX
Ref.: STRUCTURE OF THE N-GLYCOSIDASE MILB IN COMPLEX WITH HYDROXYMETHYL CMP REVEALS ITS ARG23 SPECIFICALLY RE THE SUBSTRATE AND CONTROLS ITS ENTRY NUCLEIC ACIDS RES. V. 42 8115 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5HM A:201;
Valid;
none;
submit data
353.223 C10 H16 N3 O9 P C1=C(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4OHB 2.4 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF MILB E103A IN COMPLEX WITH 5- HYDROXYMETHYLCYTIDINE 5'-MONOPHOSPHATE (HMCMP) FROM STREPTOR IMOFACIENS STREPTOMYCES RIMOFACIENS HYDROLASE PROTEIN-HMCMP COMPLEX
Ref.: STRUCTURE OF THE N-GLYCOSIDASE MILB IN COMPLEX WITH HYDROXYMETHYL CMP REVEALS ITS ARG23 SPECIFICALLY RE THE SUBSTRATE AND CONTROLS ITS ENTRY NUCLEIC ACIDS RES. V. 42 8115 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 4OHB - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
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: 5HM; Similar ligands found: 28
No: Ligand ECFP6 Tc MDL keys Tc
1 5HM 1 1
2 TKW 0.681159 0.958333
3 C5P 0.575342 0.944444
4 CAR 0.575342 0.944444
5 C 0.575342 0.944444
6 16B 0.519481 0.881579
7 5FU 0.480519 0.855263
8 CDP 0.47561 0.958333
9 CNU 0.469136 0.917808
10 5BU 0.468354 0.855263
11 ICR 0.468354 0.84
12 U5P 0.467532 0.888889
13 U 0.467532 0.888889
14 F01 0.465753 0.815789
15 HF4 0.458824 0.958333
16 CTP 0.458824 0.958333
17 7XL 0.454545 0.932432
18 JW5 0.432099 0.90411
19 C2G 0.423913 0.945205
20 NUP 0.419753 0.931507
21 UP6 0.4125 0.84
22 C5G 0.412371 0.932432
23 C C C C 0.40625 0.905405
24 5AE 0.405405 0.794521
25 BMQ 0.405063 0.837838
26 8OP 0.404494 0.810127
27 CDM 0.402062 0.884615
28 H2U 0.4 0.815789
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OHB; Ligand: 5HM; Similar sites found with APoc: 26
This union binding pocket(no: 1) in the query (biounit: 4ohb.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZRU FMN None
2 5ZI9 FLC 1.57895
3 4B5W PYR 2.63158
4 1KKR 2AS 2.63158
5 2WQ4 SFU 3.20513
6 4K7O EKZ 3.57143
7 6FTB M0E 3.68421
8 5NM7 GLY 5.6391
9 4KXL 6C6 5.92105
10 2B4B COA 6.43275
11 4XJ7 ADE 6.84211
12 1S2D ADE 7.18563
13 2GNM MAN 7.89474
14 1UKG MMA 7.89474
15 2GND MAN 7.89474
16 1Q8Q MAN MMA 7.89474
17 1Q8P MAN MMA 7.89474
18 2PHU MAN MAN 7.89474
19 3BRE C2E 8.94737
20 1F8Y 5MD 10.1911
21 1ZGS XMM 10.5263
22 2YFB SIN 11.0526
23 5AJU RP5 11.5789
24 2J5B TYE 13.1579
25 4P5E N6P 23.0263
26 4M52 M52 24.2105
Pocket No.: 2; Query (leader) PDB : 4OHB; Ligand: 5HM; 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: 4ohb.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4OHB; Ligand: 5HM; Similar sites found with APoc: 68
This union binding pocket(no: 3) in the query (biounit: 4ohb.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5NGZ 2BG None
2 2VZZ SCA 1.05263
3 1JBW TMF 1.57895
4 6F9Q NAD 2.10526
5 1ZUA NAP 2.63158
6 1ZUA TOL 2.63158
7 5UR1 YY9 2.63158
8 4O4K 2PK 2.63158
9 4CZG ADP 2.63158
10 4CZG QH3 2.63158
11 4FC7 NAP 2.63158
12 4FC7 COA 2.63158
13 3VC3 C6P 2.63158
14 5ZBL AMP 3.15789
15 5ZBK AMP 3.68421
16 4M5P FMN 3.68421
17 3IAE D7K 3.68421
18 4ITU NAI 3.68421
19 3FXU TSU 4.21053
20 1GKZ ADP 4.21053
21 1GTE IUR 4.21053
22 1GTE FMN 4.21053
23 2CFC NAD 4.21053
24 1G0N NDP 4.73684
25 1G0N PHH 4.73684
26 3O3R NAP 4.73684
27 2JB2 PHE 4.73684
28 2JB2 FAD 4.73684
29 5OBY ANP 4.73684
30 4XP7 FNR 5.20231
31 1GPE FAD 5.26316
32 3EXS 5RP 5.26316
33 2Z6J FMN 5.26316
34 1OFD AKG 5.78947
35 3LZW NAP 5.78947
36 5HSA FAS 5.78947
37 1MJH ATP 6.17284
38 1IV2 CDP 6.57895
39 1WAP TRP 6.66667
40 2BGS NDP 6.84211
41 2VVL FAD 6.84211
42 4N02 FNR 7.36842
43 6ASY ATP 7.36842
44 1JA9 NDP 7.36842
45 5OCS FMN 7.89474
46 4FWE FAD 8.42105
47 4RJK TPP 8.42105
48 5UXH GFB 8.42105
49 3PNL ADP 8.94737
50 2WKV COA 8.94737
51 5Y6Q MCN 9.25926
52 5KOR GDP 9.47368
53 1YAG ATP 10
54 5MBX FAD 10.5263
55 5MBX SP5 10.5263
56 2GAG FOA 10.5263
57 6EOF ADP 10.5263
58 4IPE ANP 12.6316
59 2FLI DX5 12.6316
60 1EKO I84 13.1579
61 1EKO NAP 13.1579
62 3HGM ATP 13.6054
63 3ZEI AWH 13.6842
64 4LRZ ADP 15.7895
65 3VKC FPQ 16.3158
66 5TTJ FAD 18.9474
67 3CR3 ADP 20
68 5G5G MCN 35.2632
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