NPASS Compound

Structure

NPC21387 OpenBabel06302216022D 30 33 0 0 1 0 0 0 0 0999 V2000 0.0023 -4.8789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8428 -4.3913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8431 -3.4157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0017 -2.9276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0015 -1.9519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -1.4638 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6914 -1.9514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8460 -0.4881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6906 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6903 0.9766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8463 1.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8466 2.4409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6926 2.9290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5383 2.4404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3837 2.9285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2289 2.4399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0950 2.9397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2286 1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3832 0.9751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5380 1.4637 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5377 0.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6920 0.9756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6917 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8457 -0.4886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6882 -2.9280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6885 -1.9524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5330 -3.4161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 28 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 26 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 26 1 0 0 0 0 11 12 2 0 0 0 0 12 23 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 21 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 23 24 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	406.32
Volume:	471.522
LogP:	6.443
LogD:	5.518
LogS:	-6.829
# Rotatable Bonds:	5
TPSA:	17.07
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.423
Synthetic Accessibility Score:	4.781
Fsp3:	0.69
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.041
MDCK Permeability:	1.7008431314025074e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.97
30% Bioavailability (F30%):	0.956

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	93.97818756103516%
Volume Distribution (VD):	1.915
Pgp-substrate:	1.9808849096298218%

ADMET: Metabolism

CYP1A2-inhibitor:	0.117
CYP1A2-substrate:	0.77
CYP2C19-inhibitor:	0.416
CYP2C19-substrate:	0.959
CYP2C9-inhibitor:	0.445
CYP2C9-substrate:	0.582
CYP2D6-inhibitor:	0.727
CYP2D6-substrate:	0.624
CYP3A4-inhibitor:	0.869
CYP3A4-substrate:	0.898

ADMET: Excretion

Clearance (CL):	2.722
Half-life (T1/2):	0.234

ADMET: Toxicity

hERG Blockers:	0.681
Human Hepatotoxicity (H-HT):	0.175
Drug-inuced Liver Injury (DILI):	0.195
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.058
Maximum Recommended Daily Dose:	0.931
Skin Sensitization:	0.972
Carcinogencity:	0.137
Eye Corrosion:	0.008
Eye Irritation:	0.112
Respiratory Toxicity:	0.962

Download Data

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

Natural Product: NPC21387

Natural Product ID:	NPC21387
*Common Name:**	GATMSTNVKBBVAI-DVXWSMRCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GATMSTNVKBBVAI-DVXWSMRCSA-N
Standard InCHI:	InChI=1S/C29H42O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h7,10-11,18-20,25,27H,8-9,12-17H2,1-6H3/b21-7+/t20-,25-,27+,28+,29-/m1/s1
SMILES:	C/C=C(CC[C@@H](C)[C@H]1CCC2=C3C=CC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C)/C(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes and derivatives

*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
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10075800]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10650102]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	Mandapam Coast, Tamilnadu, India	n.a.	PMID[22704923]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9463111]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13746	Achillea leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13746	Achillea leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16323	Umbilicaria proboscidea	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16323	Umbilicaria proboscidea	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16684	Alibertia macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13746	Achillea leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13321	Viguiera cordifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1793	Uvaria mocoli	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17210	Dorstenia barnimiana	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9044	Rubia ustulata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13985	Oxybasis urbica	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16204	Zieria chevalieri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17991	Sedum forsterianum	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7857	Verbascum georgicum	Species	Scrophulariaceae	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 NPC21387 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	219
0.1-0.2	1914
0.2-0.3	12642
0.3-0.4	15052
0.4-0.5	8300
0.5-0.6	3525
0.6-0.7	875
0.7-0.8	142
0.8-0.85	23
0.85-0.9	4
0.9-0.95	0
0.95-1	1

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 NPC21387 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	205
0.1-0.2	2126
0.2-0.3	4553
0.3-0.4	1634
0.4-0.5	342
0.5-0.6	204
0.6-0.7	69
0.7-0.8	13
0.8-0.85	1
0.85-0.9	3
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