NPASS Compound

Structure

NPC40250 OpenBabel06302215272D 35 38 0 0 1 0 0 0 0 0999 V2000 -5.8418 -1.3486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1727 -2.0917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1945 -1.8838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4514 -1.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4024 -0.9057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5254 -2.6270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8344 -3.5780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5472 -2.4190 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8781 -3.1622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2382 -1.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 -1.2601 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5909 -2.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4067 1.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5116 1.9067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1808 1.1636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6808 0.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0875 -0.6160 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7026 0.5055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 1 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 2 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 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 4 1 0 0 0 0 3 5 1 0 0 0 0 3 6 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 6 0 0 0 13 11 1 1 0 0 0 13 14 1 0 0 0 0 13 34 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 34 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 6 0 0 0 18 31 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 21 25 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 25 30 1 0 0 0 0 25 26 1 6 0 0 0 25 31 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 31 32 1 1 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	482.41
Volume:	554.769
LogP:	8.679
LogD:	6.624
LogS:	-7.356
# Rotatable Bonds:	7
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.267
Synthetic Accessibility Score:	5.579
Fsp3:	0.848
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:	-4.899
MDCK Permeability:	1.3724091331823729e-05
Pgp-inhibitor:	0.994
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.173
30% Bioavailability (F30%):	0.723

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.057
Plasma Protein Binding (PPB):	97.30362701416016%
Volume Distribution (VD):	2.122
Pgp-substrate:	1.8786159753799438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.067
CYP1A2-substrate:	0.214
CYP2C19-inhibitor:	0.135
CYP2C19-substrate:	0.956
CYP2C9-inhibitor:	0.399
CYP2C9-substrate:	0.264
CYP2D6-inhibitor:	0.043
CYP2D6-substrate:	0.451
CYP3A4-inhibitor:	0.939
CYP3A4-substrate:	0.754

ADMET: Excretion

Clearance (CL):	6.883
Half-life (T1/2):	0.014

ADMET: Toxicity

hERG Blockers:	0.991
Human Hepatotoxicity (H-HT):	0.456
Drug-inuced Liver Injury (DILI):	0.84
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.382
Maximum Recommended Daily Dose:	0.147
Skin Sensitization:	0.932
Carcinogencity:	0.134
Eye Corrosion:	0.288
Eye Irritation:	0.048
Respiratory Toxicity:	0.856

Download Data

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

Natural Product: NPC40250

Natural Product ID:	NPC40250
*Common Name:**	HDSISRBVLGLNDA-YAIXZOIGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HDSISRBVLGLNDA-YAIXZOIGSA-N
Standard InCHI:	InChI=1S/C33H54O2/c1-11-30(7,8)24(6)22(4)20-23(5)26-14-17-32(10)27-13-12-25(21(2)3)33(19-16-29(34)35-33)28(27)15-18-31(26,32)9/h22-23,25-28H,2,6,11-20H2,1,3-5,7-10H3/t22-,23-,25+,26-,27-,28+,31-,32+,33-/m1/s1
SMILES:	CCC(C)(C)C(=C)[C@H](C)C[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@@H](C(=C)C)[C@]4(CCC(=O)O4)[C@H]3CC[C@]12C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	643558
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
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15388977]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	stem	n.a.	PMID[17202689]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[20628994]
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	seeds	n.a.	n.a.	PMID[25299458]
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8744	Clematis recta	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11245	Pelvetia canaliculata	Species	Fucaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3356	Bryophyllum fedtschenkoi	Species	Spathidiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5375	Hyptis oblongifolia	Species	Lamiaceae	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 NPC40250 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	211
0.1-0.2	1894
0.2-0.3	9573
0.3-0.4	14044
0.4-0.5	6103
0.5-0.6	6773
0.6-0.7	3673
0.7-0.8	405
0.8-0.85	16
0.85-0.9	2
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 NPC40250 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	207
0.1-0.2	2306
0.2-0.3	4335
0.3-0.4	1500
0.4-0.5	404
0.5-0.6	193
0.6-0.7	180
0.7-0.8	24
0.8-0.85	1
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