Structure

Physi-Chem Properties

Molecular Weight:  262.0
Volume:  202.376
LogP:  -2.124
LogD:  -1.048
LogS:  0.132
# Rotatable Bonds:  6
TPSA:  127.2
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.523
Synthetic Accessibility Score:  5.475
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.777
MDCK Permeability:  0.0017114768270403147
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.587
20% Bioavailability (F20%):  0.935
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.667
Plasma Protein Binding (PPB):  16.23624038696289%
Volume Distribution (VD):  0.43
Pgp-substrate:  79.93960571289062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.064
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.039
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.608
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.114
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.014

ADMET: Excretion

Clearance (CL):  1.532
Half-life (T1/2):  0.797

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.011
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.036
Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.829
Skin Sensitization:  0.943
Carcinogencity:  0.288
Eye Corrosion:  0.961
Eye Irritation:  0.992
Respiratory Toxicity:  0.814

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC318351

Natural Product ID:  NPC318351
Common Name*:   (E)-4-Hydroxy-3-Methyl-But-2-Enylpyrophosphate
IUPAC Name:   [(E)-4-hydroxy-3-methylbut-2-enyl] phosphono hydrogen phosphate
Synonyms:  
Standard InCHIKey:  MDSIZRKJVDMQOQ-GORDUTHDSA-N
Standard InCHI:  InChI=1S/C5H12O8P2/c1-5(4-6)2-3-12-15(10,11)13-14(7,8)9/h2,6H,3-4H2,1H3,(H,10,11)(H2,7,8,9)/b5-2+
SMILES:  OC/C(=C/COP(=O)(OP(=O)(O)O)O)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL145233
PubChem CID:   5281976
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001311] Isoprenoid phosphates

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT111 Cell Line K562 Homo sapiens IC50 > 100000.0 nM PMID[509360]
NPT2 Others Unspecified EC50 = 0.3 nM PMID[509356]
NPT2 Others Unspecified EC50 = 0.084 nM PMID[509356]
NPT2 Others Unspecified Activity = 19700.0 n.a. PMID[509356]
NPT2 Others Unspecified EC50 = 10000.0 nM PMID[509357]
NPT2 Others Unspecified EC50 = 5300.0 nM PMID[509357]
NPT2 Others Unspecified Activity = 0.2 n.a. PMID[509357]
NPT2 Others Unspecified EC50 = 1.0 nM PMID[509358]
NPT2 Others Unspecified EC50 = 0.181 nM PMID[509358]
NPT2 Others Unspecified Activity = 21500.0 n.a. PMID[509358]
NPT2 Others Unspecified EC50 = 0.39 nM PMID[509359]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 40.0 % PMID[509359]
NPT29 Organism Rattus norvegicus Rattus norvegicus Drug uptake = 80.0 % PMID[509359]
NPT29 Organism Rattus norvegicus Rattus norvegicus Drug uptake = 50.0 % PMID[509359]
NPT35 Others n.a. AD50 = 5.0 % PMID[509359]
NPT35 Others n.a. Activity = 14.0 % PMID[509359]
NPT35 Others n.a. Activity = 4.0 % PMID[509359]
NPT2 Others Unspecified Ratio IC50/EC50 = 980.0 n.a. PMID[509360]
NPT2 Others Unspecified IC50 = 500.0 nM PMID[509360]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 0.51 nM PMID[509360]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 1.6 nM PMID[509360]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 0.06 nM PMID[509361]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens ED50 > 100.0 uM PMID[509361]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens Activity = 73.5 % PMID[509361]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 0.51 nM PMID[509362]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 0.51 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens Activity = 64.0 % PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 4.2 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 16100.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 19900.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 23000.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 > 333000.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens Kd = 1540.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens Kd = 4270.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 9640.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 12100.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 16500.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens IC50 = 4560.0 nM PMID[509363]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 0.145 nM PMID[509364]
NPT27 Others Unspecified T1/2 > 12.0 hr PMID[509364]
NPT26693 SINGLE PROTEIN Butyrophilin subfamily 3 member A1 Homo sapiens EC50 = 0.06 nM PMID[509364]
NPT2 Others Unspecified EC50 > 100000.0 nM PMID[509365]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC318351 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8718 High Similarity NPC314888
0.7234 Intermediate Similarity NPC221379
0.7179 Intermediate Similarity NPC242117
0.6977 Remote Similarity NPC315093
0.6939 Remote Similarity NPC318549
0.6744 Remote Similarity NPC314319
0.62 Remote Similarity NPC160628
0.6122 Remote Similarity NPC116934
0.5957 Remote Similarity NPC255042
0.5957 Remote Similarity NPC182840
0.5957 Remote Similarity NPC103213
0.5957 Remote Similarity NPC29091
0.5909 Remote Similarity NPC250734
0.5882 Remote Similarity NPC140501
0.5778 Remote Similarity NPC58957
0.5714 Remote Similarity NPC269823
0.5652 Remote Similarity NPC308418
0.56 Remote Similarity NPC256766
0.56 Remote Similarity NPC213538

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC318351 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6346 Remote Similarity NPD2268 Discontinued
0.5882 Remote Similarity NPD4265 Approved
0.5641 Remote Similarity NPD8559 Clinical (unspecified phase)

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data