NPASS Compound

Structure

NPC299441 OpenBabel06302215222D 26 28 0 0 1 0 0 0 0 0999 V2000 -4.0789 0.6124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7159 -0.0971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1489 -0.7662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9576 -0.3422 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0299 0.3379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4400 -0.2082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6597 -0.3809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1056 -0.1347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6597 -1.1426 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1172 -1.7265 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3544 -2.4874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3191 -2.9134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0602 -2.8576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6631 -1.5538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0760 -2.2624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8563 -2.0897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9397 -1.2713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7121 -1.1004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1946 -0.9668 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4533 -2.6211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1211 -2.1819 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4997 -3.4189 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2139 -3.7776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6597 -0.3809 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 0.8522 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 2 0 0 0 0 6 7 1 0 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:	354.15
Volume:	368.962
LogP:	4.868
LogD:	3.887
LogS:	-5.509
# Rotatable Bonds:	4
TPSA:	72.81
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.631
Synthetic Accessibility Score:	5.988
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.675
MDCK Permeability:	3.184094384778291e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.393
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.711
30% Bioavailability (F30%):	0.033

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	89.8784408569336%
Volume Distribution (VD):	1.064
Pgp-substrate:	5.746109485626221%

ADMET: Metabolism

CYP1A2-inhibitor:	0.748
CYP1A2-substrate:	0.883
CYP2C19-inhibitor:	0.1
CYP2C19-substrate:	0.634
CYP2C9-inhibitor:	0.363
CYP2C9-substrate:	0.053
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.147
CYP3A4-inhibitor:	0.386
CYP3A4-substrate:	0.291

ADMET: Excretion

Clearance (CL):	12.406
Half-life (T1/2):	0.099

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.972
Drug-inuced Liver Injury (DILI):	0.963
AMES Toxicity:	0.037
Rat Oral Acute Toxicity:	0.783
Maximum Recommended Daily Dose:	0.986
Skin Sensitization:	0.156
Carcinogencity:	0.711
Eye Corrosion:	0.003
Eye Irritation:	0.037
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC299441

Natural Product ID:	NPC299441
*Common Name:**	MVRBAGAFRPZIOR-CMDKEFSVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MVRBAGAFRPZIOR-CMDKEFSVSA-N
Standard InCHI:	InChI=1S/C21H22O5/c1-11(2)13-6-7-14-9-17(26-20(14)22)19(12(3)4)18-10-15(21(23)24-5)16(8-13)25-18/h6-7,9-10,13,17,19H,1,3,8H2,2,4-5H3/b7-6-/t13-,17-,19-/m1/s1
SMILES:	C=C(C)[C@@H]1/C=CC2=C[C@H]([C@@H](C(=C)C)c3cc(c(C1)o3)C(=O)OC)OC2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11792431
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]
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]
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]

☑ 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 NPC299441 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	312
0.1-0.2	1438
0.2-0.3	3973
0.3-0.4	9269
0.4-0.5	10163
0.5-0.6	6574
0.6-0.7	8872
0.7-0.8	1998
0.8-0.85	83
0.85-0.9	11
0.9-0.95	2
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 NPC299441 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	282
0.1-0.2	947
0.2-0.3	1780
0.3-0.4	2692
0.4-0.5	2013
0.5-0.6	1064
0.6-0.7	309
0.7-0.8	62
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