NPASS Compound

Structure

NPC47148 OpenBabel06302216102D 22 22 0 0 1 0 0 0 0 0999 V2000 2.3596 11.9909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3651 12.0954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7773 11.2864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1840 10.3729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5962 9.5639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0030 8.6503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4152 7.8413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8219 6.9278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2341 6.1187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6409 5.2052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0531 4.3962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4598 3.4826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1280 2.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2788 1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3090 0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6180 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5691 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -0.5878 0.0000 O 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 0.9511 -0.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8968 1.7601 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 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 20 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 22 1 1 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	310.25
Volume:	349.721
LogP:	6.582
LogD:	4.034
LogS:	-4.693
# Rotatable Bonds:	12
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.321
Synthetic Accessibility Score:	3.57
Fsp3:	0.842
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.707
MDCK Permeability:	2.5000475943670608e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.016
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.305
Plasma Protein Binding (PPB):	97.4142074584961%
Volume Distribution (VD):	1.55
Pgp-substrate:	2.6267735958099365%

ADMET: Metabolism

CYP1A2-inhibitor:	0.732
CYP1A2-substrate:	0.217
CYP2C19-inhibitor:	0.482
CYP2C19-substrate:	0.137
CYP2C9-inhibitor:	0.425
CYP2C9-substrate:	0.957
CYP2D6-inhibitor:	0.036
CYP2D6-substrate:	0.105
CYP3A4-inhibitor:	0.78
CYP3A4-substrate:	0.08

ADMET: Excretion

Clearance (CL):	5.167
Half-life (T1/2):	0.074

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.081
Drug-inuced Liver Injury (DILI):	0.287
AMES Toxicity:	0.034
Rat Oral Acute Toxicity:	0.113
Maximum Recommended Daily Dose:	0.011
Skin Sensitization:	0.885
Carcinogencity:	0.156
Eye Corrosion:	0.929
Eye Irritation:	0.912
Respiratory Toxicity:	0.782

Download Data

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

Natural Product: NPC47148

Natural Product ID:	NPC47148
*Common Name:**	KBHLNNQHHPFDSG-DBTFZPMKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KBHLNNQHHPFDSG-DBTFZPMKSA-N
Standard InCHI:	InChI=1S/C19H34O3/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-17-18(20)16(2)22-19(17)21/h15-16,18,20H,3-14H2,1-2H3/b17-15+/t16-,18+/m0/s1
SMILES:	CCCCCCCCCCCCC/C=C/1[C@@H]([C@H](C)OC1=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11301366
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO704	Quassia amara	Species	Simaroubaceae	Eukaryota	n.a.	leaf	n.a.	PMID[16730421]
NPO5567	Pestalotiopsis adusta	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18694644]
NPO2350	Microcos paniculata	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23327794]
NPO8569	Aiouea trinervis	Species	Lauraceae	Eukaryota	n.a.	leaf	n.a.	PMID[24634118]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2952	Schoenocaulon officinale	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO704	Quassia amara	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2952	Schoenocaulon officinale	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2350	Microcos paniculata	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO704	Quassia amara	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO704	Quassia amara	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2350	Microcos paniculata	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO844	Eperua bijuga	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6210	Eurhynchium striatum	Species	Brachytheciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7274	Strychnos psilosperma	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2350	Microcos paniculata	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8170	Hyphaene thebaica	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8468	Penaeus bennettae	Species	Penaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5567	Pestalotiopsis adusta	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3474	Gynura japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2952	Schoenocaulon officinale	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO830	Scomber japonicus	Species	Scombridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3930	Podocarpus brevifolius	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1450	Sticta coronata	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11239	Dittrichia viscosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3324	Pithomyces graminicola	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4430	Phelline brachyphylla	Species	Phellinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO704	Quassia amara	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11282	Usnea dasopoga	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8569	Aiouea trinervis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2721	Palythoa variabilis	Species	Sphenopidae	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 NPC47148 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	155
0.1-0.2	1410
0.2-0.3	6396
0.3-0.4	16223
0.4-0.5	10333
0.5-0.6	5723
0.6-0.7	1832
0.7-0.8	501
0.8-0.85	98
0.85-0.9	6
0.9-0.95	13
0.95-1	7

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 NPC47148 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	142
0.1-0.2	2149
0.2-0.3	4157
0.3-0.4	1930
0.4-0.5	578
0.5-0.6	149
0.6-0.7	41
0.7-0.8	4
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