NPASS Compound

Structure

NPC16632 OpenBabel06302215372D 25 27 0 0 1 0 0 0 0 0999 V2000 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 1 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 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 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 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 1.1340 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 0.5000 0.0000 C 0 0 2 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 -0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 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 9 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 23 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 13 1 0 0 0 0 8 9 1 0 0 0 0 8 12 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 13 21 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 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 20 1 0 0 0 0 21 18 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 6 0 0 0 23 24 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	348.23
Volume:	373.354
LogP:	4.171
LogD:	3.578
LogS:	-3.739
# Rotatable Bonds:	2
TPSA:	69.92
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.755
Synthetic Accessibility Score:	4.261
Fsp3:	0.714
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.717
MDCK Permeability:	1.530151166662108e-05
Pgp-inhibitor:	0.916
Pgp-substrate:	0.343
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.965
30% Bioavailability (F30%):	0.903

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.527
Plasma Protein Binding (PPB):	97.46182250976562%
Volume Distribution (VD):	2.743
Pgp-substrate:	3.6022701263427734%

ADMET: Metabolism

CYP1A2-inhibitor:	0.134
CYP1A2-substrate:	0.915
CYP2C19-inhibitor:	0.073
CYP2C19-substrate:	0.903
CYP2C9-inhibitor:	0.176
CYP2C9-substrate:	0.905
CYP2D6-inhibitor:	0.033
CYP2D6-substrate:	0.292
CYP3A4-inhibitor:	0.224
CYP3A4-substrate:	0.377

ADMET: Excretion

Clearance (CL):	4.42
Half-life (T1/2):	0.164

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.066
Drug-inuced Liver Injury (DILI):	0.03
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.402
Maximum Recommended Daily Dose:	0.426
Skin Sensitization:	0.814
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.084
Respiratory Toxicity:	0.935

Download Data

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

Natural Product: NPC16632

Natural Product ID:	NPC16632
*Common Name:**	GMESSRPWBYEAPG-ZWVMGRIOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GMESSRPWBYEAPG-ZWVMGRIOSA-N
Standard InCHI:	InChI=1S/C21H32O4/c1-11(2)12-10-13-14(16(23)18(12)25-6)21(5)9-7-8-20(3,4)19(21)17(24)15(13)22/h10-11,15,17,19,22-24H,7-9H2,1-6H3/t15-,17+,19+,21-/m1/s1
SMILES:	CC(C)c1cc2c(c(c1OC)O)[C@@]1(C)CCCC(C)(C)[C@@H]1[C@H]([C@@H]2O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102005790
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] 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
NPO16570	Didemnum obscurum	Species	Didemnidae	Eukaryota	n.a.	Tiruchandur coast in the Gulf of Mannar, Tamilnadu, India	2002-FEB	PMID[15270574]
NPO13852	Pachysandra terminalis	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22804108]
NPO5795	Koelpinia linearis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13852	Pachysandra terminalis	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2052	Hedyotis acutangula	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15519	Lysimachia candida	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2052	Hedyotis acutangula	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13852	Pachysandra terminalis	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5795	Koelpinia linearis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13852	Pachysandra terminalis	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21044	Sphaerellopsis filum	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18607	Eria macrophylla	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14820	Petasites spurius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16570	Didemnum obscurum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2052	Hedyotis acutangula	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18270	Betula divaricata	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27607	Saussurea candicans	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19313	Herniaria fontanesii	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15519	Lysimachia candida	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5795	Koelpinia linearis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12898	Rhaphiolepis umbellata	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19247	Viburnum jucundum	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13852	Pachysandra terminalis	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10233	Nicotiana trigonophylla	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22284	Acacia myrtifolia	Species	Fabaceae	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 NPC16632 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	423
0.1-0.2	1460
0.2-0.3	3533
0.3-0.4	8466
0.4-0.5	10360
0.5-0.6	4763
0.6-0.7	9370
0.7-0.8	3595
0.8-0.85	601
0.85-0.9	118
0.9-0.95	4
0.95-1	4

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 NPC16632 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	342
0.1-0.2	848
0.2-0.3	1784
0.3-0.4	2747
0.4-0.5	1776
0.5-0.6	963
0.6-0.7	572
0.7-0.8	111
0.8-0.85	5
0.85-0.9	2
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