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;
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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 312 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 261 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 214 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 (2D)
Ligand no: 1; Ligand: 5HM; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 5HM 1 1
2 TKW 0.681159 0.958333
3 C5P 0.575342 0.944444
4 C 0.575342 0.944444
5 CAR 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 CTP 0.458824 0.958333
16 HF4 0.458824 0.958333
17 7XL 0.454545 0.932432
18 2TM 0.448276 0.92
19 JW5 0.432099 0.90411
20 C2G 0.423913 0.945205
21 CDP MG 0.423529 0.90411
22 0RC 0.422222 0.907895
23 NUP 0.419753 0.931507
24 UP6 0.4125 0.84
25 C5G 0.412371 0.932432
26 5AE 0.405405 0.794521
27 BMQ 0.405063 0.837838
28 8OP 0.404494 0.810127
29 CDM 0.402062 0.884615
30 H2U 0.4 0.815789
Similar Ligands (3D)
Ligand no: 1; Ligand: 5HM; Similar ligands found: 67
No: Ligand Similarity coefficient
1 G 0.9627
2 TMP 0.9493
3 5GP 0.9474
4 AMP 0.9472
5 QBT 0.9456
6 5CM 0.9446
7 BRU 0.9439
8 UFP 0.9434
9 IMP 0.9408
10 5HU 0.9406
11 5IU 0.9358
12 8GM 0.9332
13 NYM 0.9297
14 NMN 0.9278
15 2DT 0.9205
16 BMP 0.9204
17 IRP 0.9200
18 8OG 0.9189
19 FN5 0.9167
20 CH 0.9167
21 DCM 0.9167
22 XMP 0.9160
23 8BR 0.9160
24 UMP 0.9140
25 FMP 0.9139
26 IMU 0.9134
27 UMC 0.9133
28 DU 0.9130
29 T3S 0.9115
30 FDM 0.9094
31 DUS 0.9082
32 71V 0.9076
33 DA 0.9057
34 D5M 0.9057
35 D4M 0.9051
36 S5P 0.9043
37 9L3 0.9014
38 DDN 0.9012
39 FNU 0.8997
40 U4S 0.8995
41 PSU 0.8989
42 DGP 0.8985
43 DG 0.8982
44 O8M 0.8978
45 U6M 0.8958
46 C2R 0.8953
47 NCN 0.8912
48 6CN 0.8909
49 35G 0.8887
50 PFU 0.8886
51 PCG 0.8885
52 75G 0.8834
53 AIR 0.8817
54 U1S 0.8796
55 U3S 0.8793
56 6J7 0.8792
57 DOC 0.8790
58 DC 0.8776
59 U2S 0.8755
60 G7M 0.8661
61 AMZ 0.8655
62 MTA 0.8598
63 3F5 0.8596
64 NEC 0.8593
65 N5O 0.8583
66 IGP 0.8551
67 A8M 0.8532
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4ohb.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4ohb.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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