NPASS Compound

Structure

NPC38639 OpenBabel06302215292D 51 55 0 0 1 0 0 0 0 0999 V2000 15.3101 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.3101 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.4595 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.6090 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.7584 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.9078 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0573 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2067 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3562 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5056 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6550 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8045 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9539 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1034 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2528 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4022 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5517 1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7011 0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8506 1.4732 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7011 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8506 -0.4911 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8506 -1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8506 -1.4732 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8506 -2.4554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8506 -0.4911 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7011 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5517 -0.4911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5517 -1.4732 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2528 -0.4911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7011 -1.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7011 -2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5517 -3.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4022 -2.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2528 -3.4375 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2528 -4.4196 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4022 -4.9107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1034 -4.9107 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1034 -5.8929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9539 -4.4196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9539 -3.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1034 -2.9464 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9539 -2.4554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1034 -1.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2528 -1.4732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4022 -1.9643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4022 -0.9821 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 0.4911 0.8506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4911 0.8506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.9464 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 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 21 48 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 51 1 1 0 0 0 24 31 1 0 0 0 0 24 25 1 1 0 0 0 24 26 1 0 0 0 0 26 27 1 1 0 0 0 26 48 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 46 1 0 0 0 0 29 30 1 1 0 0 0 29 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 46 1 0 0 0 0 35 34 1 6 0 0 0 35 36 1 0 0 0 0 35 42 1 0 0 0 0 36 37 1 1 0 0 0 36 38 1 0 0 0 0 38 39 1 6 0 0 0 38 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 1 0 0 0 42 44 1 0 0 0 0 44 45 1 0 0 0 0 45 46 1 0 0 0 0 46 47 1 6 0 0 0 48 49 1 0 0 0 0 48 50 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	706.63
Volume:	814.443
LogP:	12.747
LogD:	6.831
LogS:	-8.001
# Rotatable Bonds:	18
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.121
Synthetic Accessibility Score:	5.198
Fsp3:	0.896
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.106
MDCK Permeability:	3.5720065625355346e-06
Pgp-inhibitor:	0.194
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.188
Plasma Protein Binding (PPB):	98.51848602294922%
Volume Distribution (VD):	2.751
Pgp-substrate:	0.9043107032775879%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.164
CYP2C19-inhibitor:	0.142
CYP2C19-substrate:	0.961
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.787
CYP2D6-inhibitor:	0.175
CYP2D6-substrate:	0.011
CYP3A4-inhibitor:	0.411
CYP3A4-substrate:	0.908

ADMET: Excretion

Clearance (CL):	4.905
Half-life (T1/2):	0.005

ADMET: Toxicity

hERG Blockers:	0.979
Human Hepatotoxicity (H-HT):	0.295
Drug-inuced Liver Injury (DILI):	0.195
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.088
Maximum Recommended Daily Dose:	0.888
Skin Sensitization:	0.956
Carcinogencity:	0.049
Eye Corrosion:	0.125
Eye Irritation:	0.101
Respiratory Toxicity:	0.866

Download Data

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

Natural Product: NPC38639

Natural Product ID:	NPC38639
*Common Name:**	APLACDBFAVKPCW-CCXVAZKESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	APLACDBFAVKPCW-CCXVAZKESA-N
Standard InCHI:	InChI=1S/C48H82O3/c1-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-42(50)51-41-34-40(49)48(9)38(44(41,4)5)29-31-47(8)39(48)27-26-37-43-36(3)35(2)28-30-45(43,6)32-33-46(37,47)7/h26-27,35-36,38,40-41,43,49H,10-25,28-34H2,1-9H3/t35-,36+,38+,40-,41+,43+,45-,46-,47-,48+/m1/s1
SMILES:	CCCCCCCCCCCCCCCCCC(=O)O[C@H]1C[C@H]([C@@]2(C)[C@@H](CC[C@]3(C)C2=CC=C2[C@@H]4[C@@H](C)[C@H](C)CC[C@]4(C)CC[C@@]32C)C1(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12085701
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO12713	Brachylaena ramiflora	Species	Asteraceae	Eukaryota	twigs	Madagascar rainforest	n.a.	PMID[12193040]
NPO13045	Kielmeyera albopunctata	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762797]
NPO12713	Brachylaena ramiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26016	Spheciospongia vagabunda	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6858	Achillea tuzsonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25196	Nuxia oppositifolia	Species	Stilbaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10799	Espeletia moritziana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11869	Vernonia leopoldi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13045	Kielmeyera albopunctata	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3935	Asplenium septentrionale	Species	Aspleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5136	Colliguaja salicifolia	Species	Euphorbiaceae	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 NPC38639 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	222
0.1-0.2	1256
0.2-0.3	4316
0.3-0.4	9067
0.4-0.5	13722
0.5-0.6	6119
0.6-0.7	5287
0.7-0.8	2060
0.8-0.85	406
0.85-0.9	220
0.9-0.95	20
0.95-1	2

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 NPC38639 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	204
0.1-0.2	1504
0.2-0.3	3688
0.3-0.4	2403
0.4-0.5	874
0.5-0.6	236
0.6-0.7	217
0.7-0.8	18
0.8-0.85	4
0.85-0.9	2
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