NPASS Compound

Structure

NPC92665 OpenBabel06302216022D 31 36 0 0 1 0 0 0 0 0999 V2000 1.5068 -0.8699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5023 -0.8699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -1.7399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0045 -1.7399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5068 -0.8699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0760 -1.6533 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7655 -2.6087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9969 -1.3541 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9969 -0.3858 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8356 0.0991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6753 -1.3534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5151 -1.8376 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3542 -1.3525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1940 -1.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1946 -2.8060 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.0341 -3.2897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0344 -4.2586 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1952 -4.7437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3557 -4.2600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3554 -3.2912 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4897 -3.7917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5157 -2.8070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6770 -3.2919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8372 -2.8077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9715 -3.3082 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8367 -1.8383 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9709 -2.3388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9006 -4.7582 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0760 -0.0865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0045 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 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 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 29 1 0 0 0 0 5 6 1 0 0 0 0 5 30 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 26 1 0 0 0 0 9 10 1 0 0 0 0 9 29 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 26 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 14 15 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 17 28 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 6 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.29
Volume:	454.097
LogP:	4.514
LogD:	3.839
LogS:	-4.47
# Rotatable Bonds:	0
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.55
Synthetic Accessibility Score:	5.644
Fsp3:	0.889
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:	-4.867
MDCK Permeability:	1.0768400898086838e-05
Pgp-inhibitor:	0.904
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.865
30% Bioavailability (F30%):	0.423

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.785
Plasma Protein Binding (PPB):	82.91728973388672%
Volume Distribution (VD):	2.041
Pgp-substrate:	3.985822916030884%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.693
CYP2C19-inhibitor:	0.076
CYP2C19-substrate:	0.884
CYP2C9-inhibitor:	0.135
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.895
CYP3A4-substrate:	0.72

ADMET: Excretion

Clearance (CL):	17.073
Half-life (T1/2):	0.223

ADMET: Toxicity

hERG Blockers:	0.584
Human Hepatotoxicity (H-HT):	0.321
Drug-inuced Liver Injury (DILI):	0.557
AMES Toxicity:	0.05
Rat Oral Acute Toxicity:	0.755
Maximum Recommended Daily Dose:	0.945
Skin Sensitization:	0.948
Carcinogencity:	0.727
Eye Corrosion:	0.781
Eye Irritation:	0.308
Respiratory Toxicity:	0.99

Download Data

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

Natural Product: NPC92665

Natural Product ID:	NPC92665
*Common Name:**	YLZUMNXGXFXZNQ-SMCBIBCGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YLZUMNXGXFXZNQ-SMCBIBCGSA-N
Standard InCHI:	InChI=1S/C27H40O4/c1-15-7-10-27(30-14-15)16(2)24-22(31-27)12-21-19-6-5-17-11-18(28)8-9-25(17,3)20(19)13-23(29)26(21,24)4/h13,15-19,21-22,24,28H,5-12,14H2,1-4H3/t15-,16+,17+,18+,19-,21+,22+,24+,25+,26-,27-/m1/s1
SMILES:	C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC[C@H]6C[C@H](CC[C@]6(C)C5=CC(=O)[C@]34C)O)O2)OC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15011079
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
NPO6186	Aconitum pendulum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20506817]
NPO6186	Aconitum pendulum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26896350]
NPO8463	Brickellia arguta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6429283]
NPO6186	Aconitum pendulum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8338	Macrothelypteris oligophlebia	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8976	Agave americana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8976	Agave americana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8338	Macrothelypteris oligophlebia	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5203	Ulex minor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6186	Aconitum pendulum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17567	Blechnopsis orientalis	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6186	Aconitum pendulum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8976	Agave americana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO494	Cissampelos glaberrima	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6186	Aconitum pendulum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5203	Ulex minor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5936	Hosta montana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4605	Silene villosa	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8338	Macrothelypteris oligophlebia	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8463	Brickellia arguta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17567	Blechnopsis orientalis	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6757	Thalictrum elegans	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8976	Agave americana	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2701	Dacrydium bidwillii	Species	Mytilidae	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
IC50	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	20000.0	nM	PMID[550063]

☑ 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 NPC92665 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	231
0.1-0.2	1503
0.2-0.3	5317
0.3-0.4	10932
0.4-0.5	10127
0.5-0.6	6036
0.6-0.7	5312
0.7-0.8	3035
0.8-0.85	182
0.85-0.9	18
0.9-0.95	3
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 NPC92665 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	197
0.1-0.2	1742
0.2-0.3	4170
0.3-0.4	2062
0.4-0.5	497
0.5-0.6	187
0.6-0.7	124
0.7-0.8	155
0.8-0.85	15
0.85-0.9	1
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