NPASS Compound

Structure

NPC185907 OpenBabel06302215582D 23 24 0 0 1 0 0 0 0 0999 V2000 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 23 1 6 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 2 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	320.13
Volume:	322.398
LogP:	1.487
LogD:	2.403
LogS:	-3.069
# Rotatable Bonds:	6
TPSA:	88.38
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.757
Synthetic Accessibility Score:	2.559
Fsp3:	0.294
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.856
MDCK Permeability:	1.412803067069035e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.72
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.657
30% Bioavailability (F30%):	0.104

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.141
Plasma Protein Binding (PPB):	91.5654067993164%
Volume Distribution (VD):	0.569
Pgp-substrate:	16.945484161376953%

ADMET: Metabolism

CYP1A2-inhibitor:	0.195
CYP1A2-substrate:	0.945
CYP2C19-inhibitor:	0.138
CYP2C19-substrate:	0.825
CYP2C9-inhibitor:	0.343
CYP2C9-substrate:	0.809
CYP2D6-inhibitor:	0.189
CYP2D6-substrate:	0.905
CYP3A4-inhibitor:	0.26
CYP3A4-substrate:	0.751

ADMET: Excretion

Clearance (CL):	14.095
Half-life (T1/2):	0.897

ADMET: Toxicity

hERG Blockers:	0.076
Human Hepatotoxicity (H-HT):	0.107
Drug-inuced Liver Injury (DILI):	0.034
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.041
Maximum Recommended Daily Dose:	0.921
Skin Sensitization:	0.905
Carcinogencity:	0.065
Eye Corrosion:	0.013
Eye Irritation:	0.688
Respiratory Toxicity:	0.267

Download Data

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

Natural Product: NPC185907

Natural Product ID:	NPC185907
*Common Name:**	SCNNIVKGPABBOM-ZDUSSCGKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SCNNIVKGPABBOM-ZDUSSCGKSA-N
Standard InCHI:	InChI=1S/C17H20O6/c1-21-14-7-10(4-5-12(14)18)6-13(19)11-8-15(22-2)17(20)16(9-11)23-3/h4-5,7-9,13,18-20H,6H2,1-3H3/t13-/m0/s1
SMILES:	COc1cc(ccc1O)C[C@@H](c1cc(c(c(c1)OC)O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes

*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]
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]
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]
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]
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]

☑ 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 NPC185907 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	391
0.1-0.2	1542
0.2-0.3	4893
0.3-0.4	12535
0.4-0.5	5329
0.5-0.6	4385
0.6-0.7	7100
0.7-0.8	4697
0.8-0.85	968
0.85-0.9	509
0.9-0.95	309
0.95-1	39

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 NPC185907 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	338
0.1-0.2	877
0.2-0.3	1877
0.3-0.4	2773
0.4-0.5	1596
0.5-0.6	912
0.6-0.7	622
0.7-0.8	140
0.8-0.85	11
0.85-0.9	1
0.9-0.95	2
0.95-1	1

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