NPASS Compound

Structure

NPC179498 OpenBabel06302215572D 34 38 0 0 1 0 0 0 0 0999 V2000 1.6876 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 -0.4872 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8438 -1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 -1.4615 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8438 -2.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 -1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 -1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 -0.4872 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6876 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3753 0.9744 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2191 1.4615 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3753 1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2191 2.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0629 2.9231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9067 2.4359 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9067 1.4615 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8811 1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3939 0.6177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3683 0.6177 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0629 0.9744 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0629 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2191 -0.4872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3753 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3753 -0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7506 2.9231 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 -0.4872 0.0000 C 0 0 2 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 -0.0000 0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2191 -1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0629 -0.9744 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2191 -2.4359 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 30 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 1 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 1 0 0 0 0 9 32 1 6 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 26 1 0 0 0 0 14 23 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 28 1 1 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 19 23 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 1 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 29 10 1 6 0 0 0 29 30 1 0 0 0 0 30 31 1 1 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	472.36
Volume:	514.542
LogP:	4.763
LogD:	4.455
LogS:	-4.131
# Rotatable Bonds:	2
TPSA:	77.76
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.427
Synthetic Accessibility Score:	4.989
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.364
MDCK Permeability:	2.471933839842677e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.978
30% Bioavailability (F30%):	0.586

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.147
Plasma Protein Binding (PPB):	96.61636352539062%
Volume Distribution (VD):	0.586
Pgp-substrate:	1.9689146280288696%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.318
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.906
CYP2C9-inhibitor:	0.155
CYP2C9-substrate:	0.32
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.145
CYP3A4-inhibitor:	0.418
CYP3A4-substrate:	0.302

ADMET: Excretion

Clearance (CL):	2.612
Half-life (T1/2):	0.384

ADMET: Toxicity

hERG Blockers:	0.03
Human Hepatotoxicity (H-HT):	0.147
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.252
Maximum Recommended Daily Dose:	0.909
Skin Sensitization:	0.378
Carcinogencity:	0.02
Eye Corrosion:	0.114
Eye Irritation:	0.856
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC179498

Natural Product ID:	NPC179498
*Common Name:**	DHMLPKGHJPHKMC-TXBPDEMQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DHMLPKGHJPHKMC-TXBPDEMQSA-N
Standard InCHI:	InChI=1S/C30H48O4/c1-18-9-12-26(3)15-16-30(25(33)34)20(24(26)19(18)2)7-8-22-27(4)13-11-23(32)28(5,17-31)21(27)10-14-29(22,30)6/h7,18-19,21-24,31-32H,8-17H2,1-6H3,(H,33,34)/t18-,19+,21-,22-,23+,24+,26-,27+,28+,29-,30-/m1/s1
SMILES:	C[C@@H]1CC[C@]2(C)CC[C@@]3(C(=CC[C@@H]4[C@@]5(C)CC[C@@H]([C@@](C)(CO)[C@@H]5CC[C@@]34C)O)[C@@H]2[C@H]1C)C(=O)O
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: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
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11339628]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	bark	n.a.	PMID[17260795]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	Daejeon, Korea	2007-Jan	PMID[19670875]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[20822014]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[22547314]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	root bark	Bozhou, Anhui Province, China	2010-AUG	PMID[24377852]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	flower	n.a.	PMID[24504864]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	Flowers	LuoYang, HeNan, China	n.a.	PMID[24621197]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20825	Illicium anisatum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22745	Hedera pastuchovii	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22550	Paeonia suffruticosa	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20694	Hibiscus furcatus	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22226	Monanthotaxis fornicata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20760	Polystichum tripteron	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21022	Centaurea cineraria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20825	Illicium anisatum	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22745	Hedera pastuchovii	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21521	Xylia dolabriformis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20076	Hypoestes verticillaris	Species	Acanthaceae	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 NPC179498 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	207
0.1-0.2	1279
0.2-0.3	4643
0.3-0.4	13511
0.4-0.5	9673
0.5-0.6	5622
0.6-0.7	4814
0.7-0.8	2195
0.8-0.85	374
0.85-0.9	129
0.9-0.95	160
0.95-1	90

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 NPC179498 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	184
0.1-0.2	1624
0.2-0.3	3787
0.3-0.4	2350
0.4-0.5	731
0.5-0.6	205
0.6-0.7	192
0.7-0.8	70
0.8-0.85	3
0.85-0.9	2
0.9-0.95	2
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