Structure

Physi-Chem Properties

Molecular Weight:  326.12
Volume:  334.37
LogP:  4.634
LogD:  3.141
LogS:  -4.511
# Rotatable Bonds:  3
TPSA:  68.9
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.793
Synthetic Accessibility Score:  2.343
Fsp3:  0.211
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.687
MDCK Permeability:  1.7945669242180884e-05
Pgp-inhibitor:  0.42
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.024
Plasma Protein Binding (PPB):  93.68526458740234%
Volume Distribution (VD):  0.582
Pgp-substrate:  6.4696831703186035%

ADMET: Metabolism

CYP1A2-inhibitor:  0.766
CYP1A2-substrate:  0.967
CYP2C19-inhibitor:  0.755
CYP2C19-substrate:  0.355
CYP2C9-inhibitor:  0.839
CYP2C9-substrate:  0.901
CYP2D6-inhibitor:  0.126
CYP2D6-substrate:  0.903
CYP3A4-inhibitor:  0.378
CYP3A4-substrate:  0.395

ADMET: Excretion

Clearance (CL):  3.985
Half-life (T1/2):  0.142

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.239
Drug-inuced Liver Injury (DILI):  0.953
AMES Toxicity:  0.482
Rat Oral Acute Toxicity:  0.264
Maximum Recommended Daily Dose:  0.102
Skin Sensitization:  0.663
Carcinogencity:  0.282
Eye Corrosion:  0.003
Eye Irritation:  0.276
Respiratory Toxicity:  0.21

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  Natural Product: NPC310562

Natural Product ID:  NPC310562
Common Name*:   NHMMAMIRMITGRD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NHMMAMIRMITGRD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C19H18O5/c1-10-17(21)16-14(20)9-15(12-5-7-13(22-3)8-6-12)24-19(16)11(2)18(10)23-4/h5-9,21H,1-4H3
SMILES:  Cc1c(c2c(=O)cc(c3ccc(cc3)OC)oc2c(C)c1OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   76573
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

*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
NPO24176 Streptomyces fradiae Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[10757717]
NPO23281 Aplysinella rhax Species Aplysinellidae Eukaryota n.a. n.a. n.a. PMID[10757728]
NPO24219 Erylus nobilis Species n.a. n.a. n.a. n.a. n.a. PMID[11421740]
NPO24219 Erylus nobilis Species n.a. n.a. n.a. n.a. n.a. PMID[11908993]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[11914965]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[12350165]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. Okinawan, Japan n.a. PMID[14695804]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[15332859]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota Leaves the campus of Panjab University, Chandigarh, India PMID[16989303]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[17407351]
NPO23281 Aplysinella rhax Species Aplysinellidae Eukaryota n.a. n.a. n.a. PMID[17827010]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. fruit n.a. PMID[18020353]
NPO20637 Piper acutifolium Species Piperaceae Eukaryota n.a. leaf n.a. PMID[18712933]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. PMID[20488581]
NPO23499 Carpesium faberi Species Asteraceae Eukaryota whole plant Changshou County, Chongqing, China 2008-Aug PMID[21109433]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[22934600]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. whole plant n.a. PMID[23678820]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota Roots n.a. n.a. PMID[24054487]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24412339]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota Essential oil n.a. n.a. PMID[24641242]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[25987373]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[27116034]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[29667821]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota Fruits n.a. n.a. PMID[30543429]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota Fruits n.a. n.a. PMID[30848923]
NPO40056 Callistemon citrinus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32573227]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[7807132]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota Leaves n.a. n.a. PMID[8864235]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31132 Eucalyptus citriodora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21625 Bidens tripartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22455 Corydalis sewerzowi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21625 Bidens tripartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22455 Corydalis sewerzowi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31132 Eucalyptus citriodora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24090 Aplysilla rosea Species Darwinellidae Eukaryota n.a. Austrila n.a. Database[Title]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24249 Codonopsis cordifolioidea Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23920 Amanita pseudoporphyria Species Amanitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23413 Crematogaster africana Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23739 Staehelina fruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24290 Claviceps microcephala Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23281 Aplysinella rhax Species Aplysinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23114 Cacalia robusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23545 Vellozia streptophylla Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23043 Cryptolestes pusillus Species Laemophloeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23834 Chlamydomonas allensworthii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23884 Hippobroma longiflora Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22324 Erium villosum Species Pseudococcidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24090 Aplysilla rosea Species Darwinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24445 Arbacia pustulosa Species Arbaciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21625 Bidens tripartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23610 Aconitum tianschanicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5782 Aniba rosaeodora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23696 Solanum diflorum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO738 Dahlstedtia pentaphylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24048 Cladonia pityrea Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24219 Erylus nobilis Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24005 Mytilus galloprovincialis Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23792 Gomphostemma parviflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16043 Centaurea musimomum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13127 Vallaris heynei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20998 Machaerium kuhlmannii Species Dolichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24408 Ariocarpus fissuratus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8593 Zygosaccharomyces rouxii Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23499 Carpesium faberi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23961 Scytonema ocellatum Species Scytonemataceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18976 Centaurea arbutifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22595 Trapa bicornis Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22143 Genista sessilifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17737 Lepidorhinus squamosus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23459 Onoseris alata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12429 Acicarpha tribuloides Species Calyceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22455 Corydalis sewerzowi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21827 Albatrellus caeruleoporus Species Albatrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23211 Xyris indica Species Xyridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19535 Senecio zoellneri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20637 Piper acutifolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24176 Streptomyces fradiae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23364 Lambertella corni Species Rutstroemiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24132 Euphausia superba Species Euphausiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23318 Aconitum palmatum Species Ranunculaceae Eukaryota 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

☑ 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 NPC310562 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

  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 NPC310562 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

  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