NPASS Compound

Structure

NPC191375 OpenBabel06302215122D 32 36 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 -0.0000 -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 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0981 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6963 -3.1261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8516 -3.2860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1999 -2.7252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2833 -3.1251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4300 0.2588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9641 0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0981 1.3660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1302 0.5069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4786 -0.0539 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7625 -0.8654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2017 -1.5171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3569 -1.3573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0730 -0.5458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6338 0.1059 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -2.2321 0.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0981 1.3660 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 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 30 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 28 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 18 27 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 26 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	435.2
Volume:	449.326
LogP:	4.585
LogD:	3.665
LogS:	-4.752
# Rotatable Bonds:	2
TPSA:	68.23
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.69
Synthetic Accessibility Score:	5.37
Fsp3:	0.423
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:	-4.734
MDCK Permeability:	7.362622272921726e-05
Pgp-inhibitor:	0.032
Pgp-substrate:	0.627
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.07
30% Bioavailability (F30%):	0.654

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.448
Plasma Protein Binding (PPB):	96.22561645507812%
Volume Distribution (VD):	0.964
Pgp-substrate:	5.0244460105896%

ADMET: Metabolism

CYP1A2-inhibitor:	0.207
CYP1A2-substrate:	0.509
CYP2C19-inhibitor:	0.233
CYP2C19-substrate:	0.812
CYP2C9-inhibitor:	0.145
CYP2C9-substrate:	0.906
CYP2D6-inhibitor:	0.914
CYP2D6-substrate:	0.916
CYP3A4-inhibitor:	0.673
CYP3A4-substrate:	0.692

ADMET: Excretion

Clearance (CL):	10.137
Half-life (T1/2):	0.214

ADMET: Toxicity

hERG Blockers:	0.737
Human Hepatotoxicity (H-HT):	0.954
Drug-inuced Liver Injury (DILI):	0.906
AMES Toxicity:	0.79
Rat Oral Acute Toxicity:	0.332
Maximum Recommended Daily Dose:	0.996
Skin Sensitization:	0.941
Carcinogencity:	0.485
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.889

Download Data

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

Natural Product: NPC191375

Natural Product ID:	NPC191375
*Common Name:**	WCZWUYYJZVBKDZ-ZQMQQCDVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WCZWUYYJZVBKDZ-ZQMQQCDVSA-N
Standard InCHI:	InChI=1S/C26H29NO5/c1-30-24-14-19-20(15-25(24)31-2)22-13-18(12-17-5-3-4-10-27(17)22)32-26(29)9-7-16-6-8-23(28)21(19)11-16/h6-9,11,14-15,17-18,22,28H,3-5,10,12-13H2,1-2H3/b9-7-/t17-,18-,22-/m0/s1
SMILES:	COc1cc2-c3cc(ccc3O)/C=CC(=O)O[C@H]3C[C@@H]4CCCCN4[C@@H](C3)c2cc1OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6441299
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000221] Quinolizidines

*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
NPO12007	Pseudowintera axillaris	Species	Winteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16417306]
NPO18183	Cucumaria japonica	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[8984150]
NPO549	Musa X paradisiaca	Strain	Musaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO549	Musa X paradisiaca	Strain	Musaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO21320	Artabotrys venustus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17697	Galium glaucum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO549	Musa X paradisiaca	Strain	Musaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17697	Galium glaucum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21320	Artabotrys venustus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO549	Musa X paradisiaca	Strain	Musaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20372	Ganophyllum giganteum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21320	Artabotrys venustus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17697	Galium glaucum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18335	Vernonia stipulacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14432	Catunaregam nilotica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20295	Eclipta prostrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12007	Pseudowintera axillaris	Species	Winteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20785	Lindsaea ensifolia	Species	Lindsaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18183	Cucumaria japonica	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20520	Arenaria filicaulis	Species	Scolopacidae	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 NPC191375 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	258
0.1-0.2	1222
0.2-0.3	3689
0.3-0.4	10908
0.4-0.5	7124
0.5-0.6	8649
0.6-0.7	9776
0.7-0.8	817
0.8-0.85	250
0.85-0.9	2
0.9-0.95	0
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 NPC191375 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	169
0.1-0.2	643
0.2-0.3	922
0.3-0.4	1984
0.4-0.5	2534
0.5-0.6	1828
0.6-0.7	872
0.7-0.8	182
0.8-0.85	16
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