Structure

Physi-Chem Properties

Molecular Weight:  428.22
Volume:  443.653
LogP:  3.305
LogD:  2.617
LogS:  -4.116
# Rotatable Bonds:  1
TPSA:  86.74
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.588
Synthetic Accessibility Score:  4.069
Fsp3:  0.68
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.383
MDCK Permeability:  1.6578906070208177e-05
Pgp-inhibitor:  0.033
Pgp-substrate:  0.124
Human Intestinal Absorption (HIA):  0.875
20% Bioavailability (F20%):  0.933
30% Bioavailability (F30%):  0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  80.13912200927734%
Volume Distribution (VD):  2.005
Pgp-substrate:  11.397956848144531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.127
CYP2C19-inhibitor:  0.45
CYP2C19-substrate:  0.909
CYP2C9-inhibitor:  0.096
CYP2C9-substrate:  0.089
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.043
CYP3A4-inhibitor:  0.587
CYP3A4-substrate:  0.935

ADMET: Excretion

Clearance (CL):  2.134
Half-life (T1/2):  0.098

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.976
Drug-inuced Liver Injury (DILI):  0.989
AMES Toxicity:  0.055
Rat Oral Acute Toxicity:  0.063
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.4
Carcinogencity:  0.702
Eye Corrosion:  0.003
Eye Irritation:  0.36
Respiratory Toxicity:  0.909

Download Data

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

  Natural Product: NPC27786

Natural Product ID:  NPC27786
Common Name*:   OYIYCGXVBRNSGO-IAKYFKSNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OYIYCGXVBRNSGO-IAKYFKSNSA-N
Standard InCHI:  InChI=1S/C25H32O6/c1-11(2)25-14(12-15(26)21(3,4)19(28)23(7,8)17(12)30-25)13-16(27)22(5,6)20(29)24(9,10)18(13)31-25/h11,14H,1-10H3/t14-,25+
SMILES:  CC(C)[C@@]12[C@@H](C3=C(C(C)(C)C(=O)C(C)(C)C3=O)O1)C1=C(C(C)(C)C(=O)C(C)(C)C1=O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001816] Furofurans

*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
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. seed n.a. PMID[10661881]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. PMID[11430011]
NPO12848 Carpinus cordata Species Betulaceae Eukaryota stems n.a. n.a. PMID[12350169]
NPO15915 Edgeworthia gardneri Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[15387673]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. whole plant n.a. PMID[28294414]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16884 Convallaria keiskei Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7987 Tilia vulgaris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16642 Astrantia major Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16884 Convallaria keiskei Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7987 Tilia vulgaris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26426.1 Cassia javanica subsp. nodosa Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15697 Camellia sasanqua Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16642 Astrantia major Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7987 Tilia vulgaris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16884 Convallaria keiskei Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16557 Polygala ruwenzoriensis Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12293 Euphorbia iberica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15077 Achyranthes bidentata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13442 Eucalyptus regnans Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7987 Tilia vulgaris Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16796 Rumex conglomeratus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29027 Khaya grandifoliola Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11808 Ania latifolia Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15588 Senecio desfontainei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2038 Myrtus tomentosa Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15915 Edgeworthia gardneri Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12848 Carpinus cordata Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16642 Astrantia major Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16125 Micromonas pusilla Species Mamiellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13139 Anatheca montagnei Species Solieriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24409 Evasterias troschelii Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26426.1 Cassia javanica subsp. nodosa Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11994 Thesium humile Species Thesiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14807 Arenaria juncea Species Scolopacidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14463 Dirca occidentalis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14936 Agave shawii Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8804 Raputia simulans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5866 Bitis arietans Species Viperidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20219 Rhizobium etli Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4589 Sarcotragus spinosulus Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16884 Convallaria keiskei Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16025 Werneria decora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27733 Rosa hybrid cultivar Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO820 Grindelia perennis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9479 Ambrosia grayi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16475 Plumbago pulchella Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14313 Pachybasium candidum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2827 Plumeria alba Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15797 Drypetes littoralis Species Putranjivaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12490 Lecidea speirodes Species Lecideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15205 Alaria crispa Species Alariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11002 Hopea jucunda Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15697 Camellia sasanqua Species Theaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11987 Silene inflata Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5047 Evodiopanax innovans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16718 Pinna nobilis Species Pinnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15349 Acacia sparsiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11436 Baeomyces roseus Species Baeomycetaceae 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 14000.0 nM PMID[549990]

☑ 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 NPC27786 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 NPC27786 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