NPASS Compound

Structure

NPC284264 OpenBabel06302215072D 35 40 0 0 1 0 0 0 0 0999 V2000 1.6787 -0.0162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8256 0.4763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6789 0.9686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8253 1.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6786 1.9218 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 1.9063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8261 1.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8259 0.4768 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6517 0.9537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6517 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4771 0.4765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3030 -0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3030 -0.9539 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1561 -0.4614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1289 -1.4308 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1284 -2.3834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9813 -2.8762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3030 -2.8600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4777 -1.4305 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6245 -1.9230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6518 -0.9537 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8259 -1.4305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9537 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 0.8531 -1.4462 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7789 -0.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2951 -1.2987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3785 -1.2184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2678 -0.8770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2180 0.0743 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.9583 0.6739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8992 0.8229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5578 -0.0665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8093 1.6148 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2978 0.3209 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 1 0 0 0 0 8 7 1 1 0 0 0 8 24 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 9 1 6 0 0 0 10 21 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 19 1 0 0 0 0 13 14 1 6 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 15 26 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 1 1 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 6 0 0 0 24 2 1 6 0 0 0 26 35 1 0 0 0 0 26 27 1 6 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 1 0 0 0 30 35 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 31 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	486.33
Volume:	514.775
LogP:	3.372
LogD:	2.605
LogS:	-4.383
# Rotatable Bonds:	2
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.583
Synthetic Accessibility Score:	6.005
Fsp3:	0.933
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:	-5.291
MDCK Permeability:	1.2525003512564581e-05
Pgp-inhibitor:	0.697
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.469
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.782
Plasma Protein Binding (PPB):	74.43241119384766%
Volume Distribution (VD):	0.881
Pgp-substrate:	14.721809387207031%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.686
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.889
CYP2C9-inhibitor:	0.113
CYP2C9-substrate:	0.099
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.173
CYP3A4-inhibitor:	0.814
CYP3A4-substrate:	0.368

ADMET: Excretion

Clearance (CL):	5.965
Half-life (T1/2):	0.601

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.324
Drug-inuced Liver Injury (DILI):	0.209
AMES Toxicity:	0.05
Rat Oral Acute Toxicity:	0.951
Maximum Recommended Daily Dose:	0.888
Skin Sensitization:	0.294
Carcinogencity:	0.444
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC284264

Natural Product ID:	NPC284264
*Common Name:**	GUHNCDVCONDVGR-HPDCMKKXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GUHNCDVCONDVGR-HPDCMKKXSA-N
Standard InCHI:	InChI=1S/C30H46O5/c1-24(2)20(33)8-11-30-16-29(30)13-12-26(5)23(28(7)10-9-21(35-28)25(3,4)34)18(32)15-27(26,6)19(29)14-17(31)22(24)30/h17,19,21-23,31,34H,8-16H2,1-7H3/t17-,19+,21+,22+,23+,26-,27+,28-,29+,30-/m1/s1
SMILES:	CC1(C)C(=O)CC[C@@]23C[C@@]43CC[C@]3(C)[C@H](C(=O)C[C@@]3(C)[C@@H]4C[C@H]([C@@H]12)O)[C@@]1(C)CC[C@@H](C(C)(C)O)O1
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:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO29027	Khaya grandifoliola	Species	Meliaceae	Eukaryota	n.a.	seed	n.a.	PMID[10661881]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	n.a.	leaf	n.a.	PMID[17124632]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17124632]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17125236]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	roots	n.a.	n.a.	PMID[17125236]
NPO10682	Cystoseira mediterranea	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2045820]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5457	Dalbergia congestiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15206	Mabea fistulifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29027	Khaya grandifoliola	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12581	Corydalis densiflora	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16182	Desmodium canadense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10682	Cystoseira mediterranea	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16096	Astragalus adsurgens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15741	Embelia ribes	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1281	Schleichera trijuga	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10947	Aspilia parvifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10447	Triclisia subcordata	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7887	Schultesia guianensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5457	Dalbergia congestiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13641	Napoleonaea vogelii	Species	Lecythidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13520	Craibiodendron yunnanense	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15553	Barringtonia acutangula	Species	Lecythidaceae	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 NPC284264 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	409
0.1-0.2	3358
0.2-0.3	9755
0.3-0.4	13727
0.4-0.5	5844
0.5-0.6	5749
0.6-0.7	3011
0.7-0.8	756
0.8-0.85	74
0.85-0.9	7
0.9-0.95	7
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 NPC284264 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	432
0.1-0.2	3647
0.2-0.3	3490
0.3-0.4	959
0.4-0.5	284
0.5-0.6	235
0.6-0.7	80
0.7-0.8	23
0.8-0.85	0
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