NPASS Compound

Structure

NPC486935 OpenBabel06302215222D 29 34 0 0 1 0 0 0 0 0999 V2000 0.3515 3.7514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0077 3.7514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3358 3.1831 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6796 2.0466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8162 1.3904 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.2480 1.0620 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.6796 1.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2478 2.3746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8160 2.0466 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 2.3844 2.3748 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.9530 1.3906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3846 1.0622 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.3847 0.4061 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2482 0.4058 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2479 1.7183 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0004 2.1236 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2405 2.8619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7717 1.0617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5480 1.0615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0042 0.4333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7426 0.6731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3706 0.2166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7428 1.4494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3710 1.9056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0045 1.6895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7642 -0.3050 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2835 -0.8820 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 1.9920 3.1831 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 4 1 0 0 0 0 3 29 1 6 0 0 0 4 5 1 0 0 0 0 5 12 1 0 0 0 0 5 6 1 0 0 0 0 5 9 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 15 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 28 1 0 0 0 0 14 6 1 1 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 18 28 1 0 0 0 0 19 25 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 26 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	514.31
Volume:	535.558
LogP:	2.523
LogD:	1.96
LogS:	-3.657
# Rotatable Bonds:	19
TPSA:	145.91
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	1
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.081
Synthetic Accessibility Score:	4.605
Fsp3:	0.741
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.514
MDCK Permeability:	0.00012776016956195235
Pgp-inhibitor:	0.003
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.183
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.44
Plasma Protein Binding (PPB):	97.41240692138672%
Volume Distribution (VD):	1.087
Pgp-substrate:	2.633064031600952%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.124
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.079
CYP2C9-inhibitor:	0.031
CYP2C9-substrate:	0.119
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.077
CYP3A4-inhibitor:	0.201
CYP3A4-substrate:	0.11

ADMET: Excretion

Clearance (CL):	2.378
Half-life (T1/2):	0.937

ADMET: Toxicity

hERG Blockers:	0.202
Human Hepatotoxicity (H-HT):	0.155
Drug-inuced Liver Injury (DILI):	0.021
AMES Toxicity:	0.893
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.929
Carcinogencity:	0.627
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.487

Download Data

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

Natural Product: NPC486935

Natural Product ID:	NPC486935
*Common Name:**	WXCVDEUJZBRYIT-JUFQZULSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WXCVDEUJZBRYIT-JUFQZULSSA-N
Standard InCHI:	InChI=1S/C22H29NO6/c1-5-12(24)9-21-14-6-7-23(21)13-8-15(21)28-22(14)16(13)10(2)18(29-22)19-17(26-4)11(3)20(25)27-19/h10,12-16,24H,5-9H2,1-4H3/b19-18-/t10-,12+,13?,14?,15?,16?,21?,22-/m1/s1
SMILES:	CC[C@@H](CC12C3CCN2C2CC1O[C@@]13C2[C@@H](C)/C(=C/2C(=C(C)C(=O)O2)OC)/O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46889720
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0003305] Aminosaccharides [CHEMONTID:0000282] Aminoglycosides

*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
NPO221	Stemona aphylla	Species	Stemonaceae	Eukaryota	Roots; Stems	n.a.	n.a.	PMID[19374387]
NPO221	Stemona aphylla	Species	Stemonaceae	Eukaryota	Stems	n.a.	n.a.	PMID[20415428]
NPO221	Stemona aphylla	Species	Stemonaceae	Eukaryota	n.a.	root	n.a.	PMID[21126060]
NPO221	Stemona aphylla	Species	Stemonaceae	Eukaryota	Roots	Lampang Province, Thailand	2009-APR	PMID[21126060]
NPO221	Stemona aphylla	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21902195]
NPO221	Stemona aphylla	Species	Stemonaceae	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

Activity Type	# Activity
MIC	1

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		MIC	=	0.025	nM	PMID[20415428]

☑ 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 NPC486935 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	136
0.1-0.2	854
0.2-0.3	4841
0.3-0.4	20969
0.4-0.5	13082
0.5-0.6	2670
0.6-0.7	96
0.7-0.8	6
0.8-0.85	4
0.85-0.9	1
0.9-0.95	15
0.95-1	23

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 NPC486935 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	108
0.1-0.2	653
0.2-0.3	3229
0.3-0.4	3818
0.4-0.5	1160
0.5-0.6	174
0.6-0.7	8
0.7-0.8	0
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