NPASS Compound

Structure

NPC28116 OpenBabel06302216202D 33 37 0 0 1 0 0 0 0 0999 V2000 -3.2320 -0.4264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3150 -0.6719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0691 -1.5887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6440 -0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6443 0.9488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8230 1.4239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9492 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0005 1.8985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9446 1.9974 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8222 1.4244 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6449 0.9497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6452 0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3314 0.9746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8227 -0.4747 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8230 -1.4245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6457 -1.8991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4682 -1.4240 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2903 -1.8987 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4474 -2.3860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2909 -2.8480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1133 -3.3222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9351 -2.8471 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9346 -1.8977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9189 -1.8972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4263 -1.0450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1122 -1.4235 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1119 -0.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2898 0.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4679 -0.4742 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4676 0.4995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7878 -3.3387 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8219 2.3980 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 4 32 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 32 1 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 10 33 1 0 0 0 0 11 12 1 0 0 0 0 12 29 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 14 32 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 29 1 0 0 0 0 18 26 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 31 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	349.32
Volume:	404.704
LogP:	5.909
LogD:	3.842
LogS:	-5.129
# Rotatable Bonds:	16
TPSA:	16.35
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.231
Synthetic Accessibility Score:	2.68
Fsp3:	0.773
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.989
MDCK Permeability:	1.3912371287005953e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.774
20% Bioavailability (F20%):	0.878
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.509
Plasma Protein Binding (PPB):	69.0290298461914%
Volume Distribution (VD):	1.068
Pgp-substrate:	43.25876998901367%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.943
CYP2C19-inhibitor:	0.088
CYP2C19-substrate:	0.91
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.057
CYP2D6-inhibitor:	0.979
CYP2D6-substrate:	0.619
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.268

ADMET: Excretion

Clearance (CL):	8.09
Half-life (T1/2):	0.283

ADMET: Toxicity

hERG Blockers:	0.14
Human Hepatotoxicity (H-HT):	0.272
Drug-inuced Liver Injury (DILI):	0.039
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.849
Maximum Recommended Daily Dose:	0.038
Skin Sensitization:	0.932
Carcinogencity:	0.107
Eye Corrosion:	0.976
Eye Irritation:	0.928
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC28116

Natural Product ID:	NPC28116
*Common Name:**	TWKNDDJHVQUEJF-AJZBJTNWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TWKNDDJHVQUEJF-AJZBJTNWSA-N
Standard InCHI:	InChI=1S/C30H50O3/c1-18(2)19-10-15-30(17-31)24(33)16-29(7)20(25(19)30)8-9-22-27(5)13-12-23(32)26(3,4)21(27)11-14-28(22,29)6/h19-25,31-33H,1,8-17H2,2-7H3/t19-,20+,21-,22+,23+,24-,25+,27-,28+,29+,30-/m0/s1
SMILES:	C=C(C)[C@@H]1CC[C@]2(CO)[C@H](C[C@]3(C)[C@H](CC[C@@H]4[C@@]5(C)CC[C@H](C(C)(C)[C@@H]5CC[C@@]34C)O)[C@@H]12)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44178931
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11112781]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	n.a.	Tanzania	n.a.	PMID[11430019]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	root bark	n.a.	n.a.	PMID[12027753]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[12502337]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[153409]
NPO8106	Kadsura heteroclita	Species	Schisandraceae	Eukaryota	n.a.	stem	n.a.	PMID[16557460]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	n.a.	root	n.a.	PMID[17960072]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[17960072]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21673922]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23265519]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23317005]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23488669]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	seeds	n.a.	n.a.	PMID[26221771]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27524650]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29115831]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31287310]
NPO62	Tetracera asiatica	Species	Dilleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20434	Tolypocladium ophioglossoides	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15601	Pyrus x bretschneideri	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO62	Tetracera asiatica	Species	Dilleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8106	Kadsura heteroclita	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25151	Euphorbia cheiradenia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6313	Phormidium sp	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15601	Pyrus x bretschneideri	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15769	Solidago chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20434	Tolypocladium ophioglossoides	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5923	Bidens cernua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8408	Symphonia globulifera	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3835	Reticulitermes flavipes	Species	Termitoidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2642	Maytenus apurimacensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6076	Pentzia calva	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2309	Achillea micrantha	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO62	Tetracera asiatica	Species	Dilleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO783	Pholiota squarrosa	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1019	Citrus hybr	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3588	Crucianella maritima	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1358	Iris pallida	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8106	Kadsura heteroclita	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8278	Perenniporia ochroleuca	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20523	Bacillus subtilis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO24527	Plazia daphnoides	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 NPC28116 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	177
0.1-0.2	2247
0.2-0.3	11060
0.3-0.4	14292
0.4-0.5	5568
0.5-0.6	4148
0.6-0.7	3639
0.7-0.8	1293
0.8-0.85	150
0.85-0.9	91
0.9-0.95	10
0.95-1	22

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 NPC28116 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	168
0.1-0.2	2565
0.2-0.3	4350
0.3-0.4	1440
0.4-0.5	261
0.5-0.6	147
0.6-0.7	174
0.7-0.8	41
0.8-0.85	2
0.85-0.9	2
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