NPASS Compound

Structure

NPC205929 OpenBabel06302216202D 27 29 0 0 1 0 0 0 0 0999 V2000 -4.1091 0.6170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7435 -0.0978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1797 -0.7719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9795 -0.3447 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0450 0.3404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4507 -0.2097 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6646 -0.3837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1063 -0.1357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6646 -1.1511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1181 -1.7393 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3571 -2.5058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3215 -2.9350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0680 -2.8788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6680 -1.5653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0840 -2.2792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8701 -2.1052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9541 -1.2808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7322 -1.1086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2035 -0.9740 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4715 -2.6405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1442 -2.1981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5183 -3.4442 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2377 -3.8056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6646 -0.3837 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 -0.0000 0.8585 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8353 -0.9443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 2 1 6 0 0 0 4 5 1 0 0 0 0 4 18 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 27 1 1 0 0 0 7 25 1 0 0 0 0 7 8 2 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 24 1 0 0 0 0 10 11 1 1 0 0 0 10 14 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 14 19 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	372.16
Volume:	380.389
LogP:	3.905
LogD:	3.369
LogS:	-4.807
# Rotatable Bonds:	4
TPSA:	93.04
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.618
Synthetic Accessibility Score:	6.046
Fsp3:	0.381
Lipinski Rule-of-5:	Accepted
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:	-4.822
MDCK Permeability:	2.489449798304122e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.266
30% Bioavailability (F30%):	0.051

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.017
Plasma Protein Binding (PPB):	91.01323699951172%
Volume Distribution (VD):	0.993
Pgp-substrate:	6.515609264373779%

ADMET: Metabolism

CYP1A2-inhibitor:	0.215
CYP1A2-substrate:	0.789
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.654
CYP2C9-inhibitor:	0.334
CYP2C9-substrate:	0.407
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.327
CYP3A4-inhibitor:	0.046
CYP3A4-substrate:	0.54

ADMET: Excretion

Clearance (CL):	9.948
Half-life (T1/2):	0.248

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.961
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.838
Maximum Recommended Daily Dose:	0.996
Skin Sensitization:	0.059
Carcinogencity:	0.537
Eye Corrosion:	0.003
Eye Irritation:	0.019
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC205929

Natural Product ID:	NPC205929
*Common Name:**	MNRPADZXFBZZNX-VBRXXALCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MNRPADZXFBZZNX-VBRXXALCSA-N
Standard InCHI:	InChI=1S/C21H24O6/c1-10(2)12-6-15(22)13-8-18(27-21(13)24)19(11(3)4)17-9-14(20(23)25-5)16(7-12)26-17/h8-9,12,15,18-19,22H,1,3,6-7H2,2,4-5H3/t12-,15+,18-,19+/m1/s1
SMILES:	C=C(C)[C@@H]1C[C@@H](C2=C[C@H]([C@@H](C(=C)C)c3cc(c(C1)o3)C(=O)OC)OC2=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46222413
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000076] Furans [CHEMONTID:0004758] Furoic acid and derivatives [CHEMONTID:0004805] Furoic acid esters

*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
NPO26598	Antillogorgia acerosa	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19061360]
NPO27037	Hornschuchia obliqua	Species	Annonaceae	Eukaryota	n.a.	Brazilian	n.a.	PMID[26135746]
NPO25476	Peridinium bipes	Species	Peridiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13810	Magnolia champaca	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25476	Peridinium bipes	Species	Peridiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26012	Bothriocline calycina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25476	Peridinium bipes	Species	Peridiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26089	Vismia martiana	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24864	Senecio umgeniensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29037	Boletus peckii	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14910	Artemisia inculta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26829	Passiflora hybr	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6960	Larrea nitida	Species	Zygophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26598	Antillogorgia acerosa	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16889	Cardamine diphylla	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26569	Sigmadocia pumila	Species	Chalinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26436	Citrus glauca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13810	Magnolia champaca	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27037	Hornschuchia obliqua	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26666	Filipendula hexapetala	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26466	Eucalyptus youngiana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25898	Symplocos spicata	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25762	Lomatia tinctoria	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26762	Pachymedusa dacnicolor	Species	Hylidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23569	Roubieva multifida	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26270	Paronychia chionaea	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24034	Geraea viscida	Species	Asteraceae	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 NPC205929 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	289
0.1-0.2	1214
0.2-0.3	3456
0.3-0.4	7850
0.4-0.5	10930
0.5-0.6	6222
0.6-0.7	7336
0.7-0.8	5270
0.8-0.85	112
0.85-0.9	12
0.9-0.95	3
0.95-1	3

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 NPC205929 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	253
0.1-0.2	916
0.2-0.3	1912
0.3-0.4	2601
0.4-0.5	2076
0.5-0.6	970
0.6-0.7	321
0.7-0.8	100
0.8-0.85	1
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