NPASS Compound

Structure

NPC221212 OpenBabel06302215162D 27 32 0 0 1 0 0 0 0 0999 V2000 -0.4191 -2.1076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3921 -1.7042 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8482 -2.0585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4095 -1.9229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6535 -1.3995 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7993 -1.7347 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0046 -1.2760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1321 -0.3686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4919 0.3042 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7834 -0.7450 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7330 -1.7789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6721 -2.5904 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1464 -1.5798 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6039 -1.6141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4070 0.2355 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9240 -0.5227 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2867 -0.1547 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6017 -0.4236 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3848 -1.1267 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3509 -1.1377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5888 -0.4414 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4545 -0.1743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7473 0.6830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6532 0.6695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9203 -0.1963 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1794 -0.7178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 19 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 10 1 0 0 0 0 5 16 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 6 19 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 1 1 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 27 1 0 0 0 0 19 20 1 6 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 21 27 1 0 0 0 0 22 26 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	374.17
Volume:	365.265
LogP:	3.005
LogD:	2.869
LogS:	-4.866
# Rotatable Bonds:	3
TPSA:	67.13
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.739
Synthetic Accessibility Score:	6.808
Fsp3:	0.762
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.986
MDCK Permeability:	2.5438743250560947e-05
Pgp-inhibitor:	0.123
Pgp-substrate:	0.089
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.095

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.345
Plasma Protein Binding (PPB):	79.96804809570312%
Volume Distribution (VD):	2.104
Pgp-substrate:	15.446744918823242%

ADMET: Metabolism

CYP1A2-inhibitor:	0.035
CYP1A2-substrate:	0.975
CYP2C19-inhibitor:	0.23
CYP2C19-substrate:	0.797
CYP2C9-inhibitor:	0.234
CYP2C9-substrate:	0.043
CYP2D6-inhibitor:	0.025
CYP2D6-substrate:	0.533
CYP3A4-inhibitor:	0.783
CYP3A4-substrate:	0.319

ADMET: Excretion

Clearance (CL):	9.968
Half-life (T1/2):	0.268

ADMET: Toxicity

hERG Blockers:	0.136
Human Hepatotoxicity (H-HT):	0.365
Drug-inuced Liver Injury (DILI):	0.175
AMES Toxicity:	0.185
Rat Oral Acute Toxicity:	0.981
Maximum Recommended Daily Dose:	0.908
Skin Sensitization:	0.091
Carcinogencity:	0.203
Eye Corrosion:	0.004
Eye Irritation:	0.022
Respiratory Toxicity:	0.979

Download Data

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

Natural Product: NPC221212

Natural Product ID:	NPC221212
*Common Name:**	GRJSIUBKDJRQIL-LCVOMWBQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GRJSIUBKDJRQIL-LCVOMWBQSA-N
Standard InCHI:	InChI=1S/C21H26O6/c1-11-5-7-20-15-4-3-13(16(20)17(22)23-2)25-18(20)27-19-21(11,15)9-14(26-19)12-6-8-24-10-12/h6,8,10-11,13-16,18-19H,3-5,7,9H2,1-2H3/t11-,13-,14+,15+,16-,18+,19+,20+,21-/m1/s1
SMILES:	C[C@@H]1CC[C@]23[C@@H]4CC[C@H]([C@@H]2C(=O)OC)O[C@H]3O[C@H]2[C@]14C[C@@H](c1ccoc1)O2
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:0001551] Diterpenoids [CHEMONTID:0001757] Colensane and clerodane diterpenoids

*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
NPO17554	Schizosaccharomyces pombe	Species	Schizosaccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.3390/metabo3041118]
NPO23670	Lactuca indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762795]
NPO22221	Ibicella lutea	Species	Martyniaceae	Eukaryota	n.a.	El Volcan, Dpto. La Capital, Province of San Luis, Argentina	2001-MAR	PMID[14695802]
NPO24055	Thapsia villosa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1708405]
NPO17554	Schizosaccharomyces pombe	Species	Schizosaccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24828577]
NPO23425	Siphonodictyon coralliphagum	Species	Phloeodictyidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7673944]
NPO23670	Lactuca indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23247	Desmodium tiliaefolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24011	Gentiana pedicellata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24182	Syringa afghanica	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23042	Rhizocarpon geographicum	Species	Rhizocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23247	Desmodium tiliaefolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23670	Lactuca indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23670	Lactuca indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23228	Cladobotryum rubrobrunnescens	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23846	Pseudocedrela chevalieri	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24055	Thapsia villosa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22221	Ibicella lutea	Species	Martyniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23670	Lactuca indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24182	Syringa afghanica	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23247	Desmodium tiliaefolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22862	Stereum frustulosum	Species	Stereaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23042	Rhizocarpon geographicum	Species	Rhizocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22933	Plectranthus rugosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23425	Siphonodictyon coralliphagum	Species	Phloeodictyidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21446	Burchellia bubalina	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22986	Perezia hebeclada	Species	Pereziidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24458	Sindora sumatrana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24011	Gentiana pedicellata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20639	Lupinus palmeri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17554	Schizosaccharomyces pombe	Species	Schizosaccharomycetaceae	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 NPC221212 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	414
0.1-0.2	1465
0.2-0.3	3152
0.3-0.4	6138
0.4-0.5	11454
0.5-0.6	11303
0.6-0.7	7767
0.7-0.8	766
0.8-0.85	190
0.85-0.9	41
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 NPC221212 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	345
0.1-0.2	943
0.2-0.3	2142
0.3-0.4	2781
0.4-0.5	1961
0.5-0.6	770
0.6-0.7	198
0.7-0.8	8
0.8-0.85	2
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