NPASS Compound

Structure

NPC59500 OpenBabel06302215282D 27 32 0 0 1 0 0 0 0 0999 V2000 -2.5999 -3.2446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4671 -2.7436 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4668 -1.7664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3129 -1.2776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1593 -1.7660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0050 -1.2774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8514 -1.7658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8517 -2.7430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0061 -3.2316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1596 -2.7432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3135 -3.2320 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3138 -4.2092 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7396 -4.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8522 -4.6961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6978 -4.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6981 -3.2314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3129 -0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4668 0.1870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6206 -0.3018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7748 0.1865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9289 -0.3018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9289 -1.2785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7748 -1.7669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6206 -1.2785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.5804 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5741 -0.7902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 1 0 0 0 0 3 24 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 17 2 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 16 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 1 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 24 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 27 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	363.11
Volume:	354.29
LogP:	4.649
LogD:	3.357
LogS:	-7.406
# Rotatable Bonds:	1
TPSA:	49.39
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.65
Synthetic Accessibility Score:	3.399
Fsp3:	0.238
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:	-4.9
MDCK Permeability:	5.1124112360412255e-05
Pgp-inhibitor:	0.487
Pgp-substrate:	0.03
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.024

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.054
Plasma Protein Binding (PPB):	95.90504455566406%
Volume Distribution (VD):	0.596
Pgp-substrate:	0.9312568306922913%

ADMET: Metabolism

CYP1A2-inhibitor:	0.98
CYP1A2-substrate:	0.29
CYP2C19-inhibitor:	0.971
CYP2C19-substrate:	0.209
CYP2C9-inhibitor:	0.765
CYP2C9-substrate:	0.894
CYP2D6-inhibitor:	0.982
CYP2D6-substrate:	0.909
CYP3A4-inhibitor:	0.868
CYP3A4-substrate:	0.17

ADMET: Excretion

Clearance (CL):	15.263
Half-life (T1/2):	0.087

ADMET: Toxicity

hERG Blockers:	0.063
Human Hepatotoxicity (H-HT):	0.06
Drug-inuced Liver Injury (DILI):	0.923
AMES Toxicity:	0.856
Rat Oral Acute Toxicity:	0.106
Maximum Recommended Daily Dose:	0.945
Skin Sensitization:	0.869
Carcinogencity:	0.969
Eye Corrosion:	0.003
Eye Irritation:	0.252
Respiratory Toxicity:	0.929

Download Data

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

Natural Product: NPC59500

Natural Product ID:	NPC59500
*Common Name:**	MHPDDMNAUJQRSW-NRFANRHFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MHPDDMNAUJQRSW-NRFANRHFSA-N
Standard InCHI:	InChI=1S/C21H17NO5/c1-22-19-13(4-3-11-7-16-17(8-14(11)19)26-9-25-16)12-5-6-15-20(27-10-24-15)18(12)21(22)23-2/h3-8,21H,9-10H2,1-2H3/t21-/m0/s1
SMILES:	CN1c2c(-c3ccc4c(c3[C@@H]1OC)OCO4)ccc1cc3c(cc21)OCO3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002665] Benzophenanthridine alkaloids [CHEMONTID:0002667] Dihydrobenzophenanthridine alkaloids

*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
NPO24024	Fusarium semitectum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10978211]
NPO21424	Garcinia xanthochymus	Species	Clusiaceae	Eukaryota	n.a.	xylem	n.a.	PMID[14600386]
NPO21424	Garcinia xanthochymus	Species	Clusiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[15787435]
NPO24024	Fusarium semitectum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22439674]
NPO18823	Colysis pothifolia	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26731047]
NPO21424	Garcinia xanthochymus	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21004	Nicotiana plumbaginifolia	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20871	Pueraria tuberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21424	Garcinia xanthochymus	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21004	Nicotiana plumbaginifolia	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20871	Pueraria tuberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20871	Pueraria tuberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19340	Orobanche caerulescens	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15221	Crambe fruticosa	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21143	Cryptocarya canelilla	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23296	Teucrium carolipaui	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21230	Heterodermia obscurata	Species	Physciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25505	Astilbe japonica	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21004	Nicotiana plumbaginifolia	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18580	Diabelia spathulata	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13216	Streptomyces pulveraceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO20871	Pueraria tuberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25619	Vitex divaricata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18421	Tachardia lacca	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20271	Canarina canariensis	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18613	Commiphora erlangeriana	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21677	Liatris aspera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21424	Garcinia xanthochymus	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18823	Colysis pothifolia	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24024	Fusarium semitectum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8315	Wunderlichia crulsiana	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 NPC59500 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	472
0.1-0.2	2362
0.2-0.3	10770
0.3-0.4	6770
0.4-0.5	9708
0.5-0.6	10354
0.6-0.7	1628
0.7-0.8	564
0.8-0.85	50
0.85-0.9	9
0.9-0.95	5
0.95-1	5

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 NPC59500 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	254
0.1-0.2	804
0.2-0.3	1012
0.3-0.4	1755
0.4-0.5	2901
0.5-0.6	1938
0.6-0.7	446
0.7-0.8	40
0.8-0.85	0
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