NPASS Compound

Structure

NPC4401 OpenBabel06302215442D 28 30 0 0 1 0 0 0 0 0999 V2000 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 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 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 23 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 21 1 0 0 0 0 8 9 1 0 0 0 0 9 19 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 20 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 19 1 0 0 0 0 13 14 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 18 1 0 0 0 0 18 19 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 23 28 1 6 0 0 0 24 25 1 0 0 0 0 24 27 1 6 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.12
Volume:	378.037
LogP:	0.779
LogD:	0.778
LogS:	-3.509
# Rotatable Bonds:	6
TPSA:	129.59
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.468
Synthetic Accessibility Score:	3.44
Fsp3:	0.25
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:	-5.391
MDCK Permeability:	8.85013650986366e-06
Pgp-inhibitor:	0.01
Pgp-substrate:	0.587
Human Intestinal Absorption (HIA):	0.149
20% Bioavailability (F20%):	0.078
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.315
Plasma Protein Binding (PPB):	75.34776306152344%
Volume Distribution (VD):	1.02
Pgp-substrate:	19.461162567138672%

ADMET: Metabolism

CYP1A2-inhibitor:	0.158
CYP1A2-substrate:	0.925
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.077
CYP2C9-inhibitor:	0.024
CYP2C9-substrate:	0.654
CYP2D6-inhibitor:	0.075
CYP2D6-substrate:	0.338
CYP3A4-inhibitor:	0.303
CYP3A4-substrate:	0.268

ADMET: Excretion

Clearance (CL):	10.962
Half-life (T1/2):	0.434

ADMET: Toxicity

hERG Blockers:	0.06
Human Hepatotoxicity (H-HT):	0.717
Drug-inuced Liver Injury (DILI):	0.97
AMES Toxicity:	0.301
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.02
Skin Sensitization:	0.038
Carcinogencity:	0.05
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.032

Download Data

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

Natural Product: NPC4401

Natural Product ID:	NPC4401
*Common Name:**	CLCRLPWALDAQJW-YJYMSZOUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CLCRLPWALDAQJW-YJYMSZOUSA-N
Standard InCHI:	InChI=1S/C20H20O8/c1-26-14-7-11(19(25)13(23)9-21)8-15(27-2)18(14)17-12(22)5-3-10-4-6-16(24)28-20(10)17/h3-8,13,19,21-23,25H,9H2,1-2H3/t13-,19+/m1/s1
SMILES:	COc1cc(cc(c1c1c(ccc2ccc(=O)oc12)O)OC)[C@@H]([C@@H](CO)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0002908] Hydroxycoumarins [CHEMONTID:0002909] 7-hydroxycoumarins

*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
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10092191]
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10724012]
NPO28843	Astragalus zahlbruckneri	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[11575952]
NPO24786	Eunicea pinta	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350138]
NPO1145	Coussarea paniculata	Species	Rubiaceae	Eukaryota	twigs	n.a.	n.a.	PMID[12662105]
NPO22193	Ophioglossum petiolatum	Species	Ophioglossaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[15787440]
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15787462]
NPO28797	Hypoxylon carneum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16933875]
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9066761]
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9249977]
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9510911]
NPO25033	Pyrola calliantha	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25414	Solanum berthaultii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25033	Pyrola calliantha	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25414	Solanum berthaultii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25033	Pyrola calliantha	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7329	Ligularia pleurocaulis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24786	Eunicea pinta	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24554	Hymenocallis speciosa	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25414	Solanum berthaultii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13482	Nierembergia hippomanica	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24984	Hydrocotyle leucocephala	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25033	Pyrola calliantha	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22193	Ophioglossum petiolatum	Species	Ophioglossaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25289	Lonchocarpus salvadorensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25563	Axinella cannabina	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23383	Nigritella suaveolens	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO24637	Oyedaea verbesinoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24066	0cardia brasiliensis	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO24203	Sphoeroides vermicularis	Species	Tetraodontidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28797	Hypoxylon carneum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1145	Coussarea paniculata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25233	Crocodylus niloticus	Species	Crocodylidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28843	Astragalus zahlbruckneri	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 NPC4401 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	379
0.1-0.2	1601
0.2-0.3	3723
0.3-0.4	8388
0.4-0.5	10010
0.5-0.6	3859
0.6-0.7	5190
0.7-0.8	4690
0.8-0.85	3199
0.85-0.9	1519
0.9-0.95	139
0.95-1	0

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 NPC4401 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	358
0.1-0.2	924
0.2-0.3	1734
0.3-0.4	2537
0.4-0.5	1928
0.5-0.6	1060
0.6-0.7	391
0.7-0.8	137
0.8-0.85	59
0.85-0.9	21
0.9-0.95	1
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