NPASS Compound

Structure

NPC238954 OpenBabel06302215352D 37 41 0 0 1 0 0 0 0 0999 V2000 3.3816 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3816 0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2270 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5362 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8454 1.4643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8454 -0.4881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8454 -1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 -1.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8454 -2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 -0.4881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6908 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5362 -0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5362 -1.4643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2270 -0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6908 -1.9524 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6908 -2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5362 -3.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3816 -2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2270 -3.4167 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2270 -4.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0724 -4.8810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5605 -5.7264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5843 -5.7264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9178 -4.3929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9178 -3.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0724 -2.9286 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9178 -2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0724 -1.9524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2270 -1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3816 -1.9524 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3816 -0.9762 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 0.4881 0.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4881 0.8454 0.0000 C 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 35 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 18 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 1 0 0 0 13 35 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 33 1 0 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 19 1 1 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 33 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 6 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 24 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 1 0 0 0 29 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 6 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	510.44
Volume:	583.441
LogP:	9.048
LogD:	6.707
LogS:	-7.774
# Rotatable Bonds:	4
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.279
Synthetic Accessibility Score:	4.669
Fsp3:	0.914
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.055
MDCK Permeability:	9.507126378593966e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.121
30% Bioavailability (F30%):	0.752

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.027
Plasma Protein Binding (PPB):	94.34773254394531%
Volume Distribution (VD):	1.276
Pgp-substrate:	2.243316888809204%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.162
CYP2C19-inhibitor:	0.104
CYP2C19-substrate:	0.953
CYP2C9-inhibitor:	0.112
CYP2C9-substrate:	0.628
CYP2D6-inhibitor:	0.043
CYP2D6-substrate:	0.342
CYP3A4-inhibitor:	0.415
CYP3A4-substrate:	0.621

ADMET: Excretion

Clearance (CL):	4.719
Half-life (T1/2):	0.024

ADMET: Toxicity

hERG Blockers:	0.035
Human Hepatotoxicity (H-HT):	0.199
Drug-inuced Liver Injury (DILI):	0.03
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.046
Maximum Recommended Daily Dose:	0.904
Skin Sensitization:	0.737
Carcinogencity:	0.018
Eye Corrosion:	0.098
Eye Irritation:	0.177
Respiratory Toxicity:	0.942

Download Data

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

Natural Product: NPC238954

Natural Product ID:	NPC238954
*Common Name:**	ZYZHOJHOPCBGMY-YJRFALJNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZYZHOJHOPCBGMY-YJRFALJNSA-N
Standard InCHI:	InChI=1S/C35H58O2/c1-23(2)21-29(36)37-28-14-15-33(8)26(31(28,5)6)13-16-35(10)27(33)12-11-24-25-22-30(3,4)17-18-32(25,7)19-20-34(24,35)9/h11,23,25-28H,12-22H2,1-10H3/t25-,26-,27+,28-,32+,33-,34+,35+/m0/s1
SMILES:	CC(C)CC(=O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)CC[C@]4(C)CC[C@@]32C)C1(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
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
NPO17048	Jungermannia subulata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11999396]
NPO16027	Niphogeton ternata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18366	Papaver commutatum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16027	Niphogeton ternata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15580	Justicia simplex	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18366	Papaver commutatum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18366	Papaver commutatum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15580	Justicia simplex	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16027	Niphogeton ternata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16421	Chalciporus piperatus	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5062	Aristolochia tagala	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2066	Streptomyces ipomoeae	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7166	Streptomyces aureus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15832	Ruscus hypophyllum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13892	Calea clausseniana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16631	Libocedrus yateensis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15580	Justicia simplex	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO426	Camellia reticulata	Species	Theaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17933	Cylicodaphne sebifera	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO17488	Rhoiptelea chiliantha	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17048	Jungermannia subulata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18903	Chromodoris willani	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17264	Mycena haematopus	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18366	Papaver commutatum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18434	Dactylosporangium aurantiacum	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17168	Ageratina riparia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16942	Asparagus thunbergianus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18044	Lotus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11999	Piptadenia peregrina	Species	Fabaceae	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 NPC238954 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	229
0.1-0.2	1578
0.2-0.3	6017
0.3-0.4	16697
0.4-0.5	7088
0.5-0.6	5071
0.6-0.7	4532
0.7-0.8	1115
0.8-0.85	224
0.85-0.9	114
0.9-0.95	20
0.95-1	12

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 NPC238954 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	1822
0.2-0.3	4208
0.3-0.4	2036
0.4-0.5	485
0.5-0.6	223
0.6-0.7	144
0.7-0.8	18
0.8-0.85	2
0.85-0.9	4
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