Structure

Physi-Chem Properties

Molecular Weight:  680.2
Volume:  695.555
LogP:  6.157
LogD:  3.484
LogS:  -3.686
# Rotatable Bonds:  4
TPSA:  182.07
# H-Bond Aceptor:  9
# H-Bond Donor:  9
# Rings:  8
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.09
Synthetic Accessibility Score:  4.376
Fsp3:  0.095
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.181
MDCK Permeability:  5.938677531958092e-06
Pgp-inhibitor:  0.354
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.934
20% Bioavailability (F20%):  0.943
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  93.2232437133789%
Volume Distribution (VD):  0.577
Pgp-substrate:  5.078273773193359%

ADMET: Metabolism

CYP1A2-inhibitor:  0.769
CYP1A2-substrate:  0.398
CYP2C19-inhibitor:  0.954
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.813
CYP2C9-substrate:  0.997
CYP2D6-inhibitor:  0.241
CYP2D6-substrate:  0.422
CYP3A4-inhibitor:  0.558
CYP3A4-substrate:  0.311

ADMET: Excretion

Clearance (CL):  11.052
Half-life (T1/2):  0.524

ADMET: Toxicity

hERG Blockers:  0.182
Human Hepatotoxicity (H-HT):  0.09
Drug-inuced Liver Injury (DILI):  0.47
AMES Toxicity:  0.079
Rat Oral Acute Toxicity:  0.771
Maximum Recommended Daily Dose:  0.996
Skin Sensitization:  0.974
Carcinogencity:  0.013
Eye Corrosion:  0.003
Eye Irritation:  0.899
Respiratory Toxicity:  0.051

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

  Natural Product: NPC297948

Natural Product ID:  NPC297948
Common Name*:   QSNCUGULHPBRGR-FYPZSMAZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QSNCUGULHPBRGR-FYPZSMAZSA-N
Standard InCHI:  InChI=1S/C16H25NO3/c1-8(2)10-11-14(18)20-12(10)13-15(3)9(7-17(13)4)5-6-16(11,15)19/h8-13,19H,5-7H2,1-4H3/p+1/t9-,10+,11-,12-,13-,15-,16-/m1/s1
SMILES:  CC(C)[C@H]1[C@@H]2C(=O)O[C@H]1[C@@H]1[C@@]3(C)[C@H](CC[C@@]23O)C[NH+]1C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives

*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
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[11575955]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[16268553]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. Fijian red alga n.a. PMID[16724831]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota stems Yunnan Province, China 2004 PMID[17253844]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[17715978]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems purchased from Kyoungdong Oriental Herbal Market, Seoul, Korea 2006-APR PMID[18052323]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. Fijian red alga n.a. PMID[20141173]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems n.a. n.a. PMID[27310249]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[30407005]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO23740 Jacobaea analoga Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1575 Mikania luetzelburgii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6178 Solanum euacanthum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13053 Corydalis conspersa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO326 Pittosporum brevicalyx Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15662 Ligustrum ovalifolium Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23740 Jacobaea analoga Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4581 Ungernia victoris Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15280 Sideritis grandiflora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5019 Mespilus germanica Species Rosaceae 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 NPC297948 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 NPC297948 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