NPASS Compound

Structure

NPC200396 OpenBabel06302215332D 32 36 0 0 1 0 0 0 0 0999 V2000 0.1242 4.6336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0791 5.5886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6463 6.2421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0078 5.8900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2110 6.8450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7332 5.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6619 5.5379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3873 4.8844 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3160 5.1859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3870 3.9080 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2322 3.4191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2319 2.4423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5401 2.4428 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6935 1.9543 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8472 2.4433 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8474 3.4200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6941 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5404 3.4196 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5407 4.4196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 1.9548 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0008 2.9548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8452 2.4437 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6912 1.9553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6915 0.9779 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8458 0.4890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9774 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8466 0.4885 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6932 0.9769 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5591 0.4767 0.0000 O 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 2.5577 0.4783 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 3.4437 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 2 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 10 18 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 13 18 1 0 0 0 0 14 15 1 0 0 0 0 14 28 1 0 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 20 26 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 22 32 1 1 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 31 1 6 0 0 0 26 25 1 1 0 0 0 26 30 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 27 30 1 6 0 0 0 28 29 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	444.32
Volume:	479.95
LogP:	4.453
LogD:	4.534
LogS:	-4.5
# Rotatable Bonds:	4
TPSA:	73.22
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.441
Synthetic Accessibility Score:	5.894
Fsp3:	0.857
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:	-4.801
MDCK Permeability:	2.562915688031353e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.987
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.024
30% Bioavailability (F30%):	0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.4
Plasma Protein Binding (PPB):	93.80648803710938%
Volume Distribution (VD):	1.52
Pgp-substrate:	3.046807289123535%

ADMET: Metabolism

CYP1A2-inhibitor:	0.086
CYP1A2-substrate:	0.428
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.791
CYP2C9-inhibitor:	0.163
CYP2C9-substrate:	0.061
CYP2D6-inhibitor:	0.022
CYP2D6-substrate:	0.481
CYP3A4-inhibitor:	0.827
CYP3A4-substrate:	0.452

ADMET: Excretion

Clearance (CL):	9.425
Half-life (T1/2):	0.42

ADMET: Toxicity

hERG Blockers:	0.558
Human Hepatotoxicity (H-HT):	0.244
Drug-inuced Liver Injury (DILI):	0.114
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.921
Maximum Recommended Daily Dose:	0.963
Skin Sensitization:	0.577
Carcinogencity:	0.256
Eye Corrosion:	0.04
Eye Irritation:	0.026
Respiratory Toxicity:	0.985

Download Data

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

Natural Product: NPC200396

Natural Product ID:	NPC200396
*Common Name:**	HKVZMOJMCNBQFH-OUYYDURMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HKVZMOJMCNBQFH-OUYYDURMSA-N
Standard InCHI:	InChI=1S/C28H44O4/c1-15(2)16(3)7-8-17(4)19-9-10-20-23-21(11-12-26(19,20)5)27(6)22(30)13-18(29)14-28(27)25(32-28)24(23)31/h7-8,15,17-25,29-31H,3,9-14H2,1-2,4-6H3/b8-7+/t17-,18+,19-,20+,21+,22+,23+,24-,25-,26-,27+,28-/m1/s1
SMILES:	CC(C)C(=C)/C=C/[C@@H](C)[C@H]1CC[C@H]2[C@H]3[C@H](CC[C@]12C)[C@@]1(C)[C@H](C[C@@H](C[C@]21[C@@H]([C@@H]3O)O2)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	16656567
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003567] Ergostane steroids

*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
NPO24056	Sinularia grandilobata	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18447385]
NPO24255	Chaetomium elatum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23586920]
NPO4192	Gynochthodes umbellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23968	Paris verticillata	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17563	Chroococcus turgidus	Species	Chroococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23762	Callicarpa dichotoma	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24099	Isodon oresbius	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24012	Senecio longiflorus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24255	Chaetomium elatum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24056	Sinularia grandilobata	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22167	Fossombronia pusilla	Species	Fossombroniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23635	Ehretia aspera	Species	Ehretiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21715	Leymus mollis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4192	Gynochthodes umbellata	Species	Rubiaceae	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 NPC200396 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	238
0.1-0.2	1361
0.2-0.3	5265
0.3-0.4	12573
0.4-0.5	10925
0.5-0.6	5466
0.6-0.7	5359
0.7-0.8	1402
0.8-0.85	88
0.85-0.9	17
0.9-0.95	3
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 NPC200396 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	200
0.1-0.2	1467
0.2-0.3	4261
0.3-0.4	2215
0.4-0.5	575
0.5-0.6	216
0.6-0.7	186
0.7-0.8	28
0.8-0.85	2
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