NPASS Compound

Structure

NPC4612 OpenBabel06302216132D 27 29 0 0 1 0 0 0 0 0999 V2000 5.0733 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6665 -1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6720 -0.9781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 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 2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 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 0.0000 2.0000 0.0000 C 0 0 2 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 1 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 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 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 0.0000 3.0000 0.0000 O 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 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0029 -1.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0247 -1.5134 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3119 -2.6723 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 25 1 0 0 0 0 4 5 1 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 22 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 6 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 13 1 0 0 0 0 12 21 1 0 0 0 0 13 14 1 0 0 0 0 13 20 1 6 0 0 0 14 15 1 0 0 0 0 14 19 1 0 0 0 0 15 16 1 6 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	390.12
Volume:	348.406
LogP:	-0.319
LogD:	-0.065
LogS:	-0.755
# Rotatable Bonds:	5
TPSA:	183.21
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.301
Synthetic Accessibility Score:	4.605
Fsp3:	0.75
Lipinski Rule-of-5:	Rejected
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:	-6.352
MDCK Permeability:	0.00012784457067027688
Pgp-inhibitor:	0.0
Pgp-substrate:	0.027
Human Intestinal Absorption (HIA):	0.939
20% Bioavailability (F20%):	0.049
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.237
Plasma Protein Binding (PPB):	20.820110321044922%
Volume Distribution (VD):	0.256
Pgp-substrate:	51.650779724121094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.026
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.04
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.076
CYP2D6-inhibitor:	0.03
CYP2D6-substrate:	0.084
CYP3A4-inhibitor:	0.012
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	1.444
Half-life (T1/2):	0.918

ADMET: Toxicity

hERG Blockers:	0.023
Human Hepatotoxicity (H-HT):	0.171
Drug-inuced Liver Injury (DILI):	0.914
AMES Toxicity:	0.026
Rat Oral Acute Toxicity:	0.027
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.103
Carcinogencity:	0.827
Eye Corrosion:	0.003
Eye Irritation:	0.049
Respiratory Toxicity:	0.576

Download Data

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

Natural Product: NPC4612

Natural Product ID:	NPC4612
*Common Name:**	CBXLCEGPMWRVQS-ALJFVJQCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CBXLCEGPMWRVQS-ALJFVJQCSA-N
Standard InCHI:	InChI=1S/C16H22O11/c17-3-8-10(18)11(19)12(20)16(26-8)27-15-9-5(1-2-6(9)13(21)22)7(4-25-15)14(23)24/h4-6,8-12,15-20H,1-3H2,(H,21,22)(H,23,24)/t5-,6+,8-,9+,10-,11+,12-,15+,16+/m1/s1
SMILES:	C1C[C@@H]([C@@H]2[C@H]1C(=CO[C@H]2O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15559328
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-glycosides

*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
NPO1766	Hymenaea courbaril	Species	Fabaceae	Eukaryota	n.a.	Suriname rain forest	n.a.	PMID[11809056]
NPO6779	Sutherlandia frutescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18808182]
NPO5985	Klebsiella pneumoniae	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24572278]
NPO6381	Dendrobium crepidatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26710212]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7812	Alhagi persarum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8312	Polygonatum stenophyllum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8175	Acacia kempeana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5985	Klebsiella pneumoniae	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2525	Castanopsis cuspidata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2366	Diospyros buxifolia	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8476	Teucrium lanigerum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO850	Metatrichia vesparium	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6381	Dendrobium crepidatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2218	Aframomum sulcatum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5039	Cryptomonas ovata	Species	Cryptomonadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3944	Senecio variabilis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4271	Dendrobium thyrsiflorum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7601	Centaurea cana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5235	Laburnum watereri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22995	Oophaga histrionica	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6979	Baillonella toxisperma	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26373.1	Microbispora rosea subsp. aerata	Subspecies	Streptosporangiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4644	Pteris pacifica	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4096	Acanthias vulgaris	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3672	Montanoa guatemalensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1766	Hymenaea courbaril	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO720	Badilloa salicina	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6779	Sutherlandia frutescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2011	Decaisnea fargesii	Species	Lardizabalaceae	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 NPC4612 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	227
0.1-0.2	1476
0.2-0.3	5456
0.3-0.4	11282
0.4-0.5	11021
0.5-0.6	7691
0.6-0.7	5113
0.7-0.8	387
0.8-0.85	24
0.85-0.9	3
0.9-0.95	17
0.95-1	0

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 NPC4612 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	231
0.1-0.2	2101
0.2-0.3	3906
0.3-0.4	1921
0.4-0.5	566
0.5-0.6	321
0.6-0.7	103
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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