NPASS Compound

Structure

CID147232 OpenBabel06191715522D 35 39 0 0 1 0 0 0 0 0999 V2000 5.0662 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5081 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0206 0.6181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8650 0.8444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6887 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8444 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -0.4875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3775 -1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8444 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6887 -1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -0.4875 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6887 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 2.9250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 0.9750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 0.9750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5331 -0.4875 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5331 2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5331 -2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5331 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 1.4625 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8444 -0.4875 0.0000 C 0 0 1 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 3.3775 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5331 -1.4625 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6887 3.9000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3775 2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6887 -2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3775 -2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8900 0.8444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 25 1 0 0 0 0 3 25 1 0 0 0 0 5 27 1 0 0 0 0 8 9 1 0 0 0 0 8 18 2 0 0 0 0 9 21 1 0 0 0 0 10 13 1 0 0 0 0 10 17 1 0 0 0 0 11 12 1 0 0 0 0 11 20 1 0 0 0 0 12 28 1 0 0 0 0 13 30 1 0 0 0 0 14 15 1 0 0 0 0 14 27 1 0 0 0 0 15 30 1 0 0 0 0 16 19 2 0 0 0 0 16 26 1 0 0 0 0 17 29 1 6 0 0 0 18 22 1 0 0 0 0 18 27 1 0 0 0 0 19 23 1 0 0 0 0 19 31 1 0 0 0 0 20 25 1 0 0 0 0 20 26 1 1 0 0 0 21 26 1 1 0 0 0 21 28 1 0 0 0 0 22 29 1 6 0 0 0 22 30 1 0 0 0 0 23 25 1 0 0 0 0 23 32 2 0 0 0 0 24 33 2 0 0 0 0 24 34 1 0 0 0 0 26 4 1 1 0 0 0 27 28 1 1 0 0 0 28 6 1 1 0 0 0 29 7 1 1 0 0 0 29 35 1 0 0 0 0 30 24 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	484.32
Volume:	518.059
LogP:	4.712
LogD:	4.252
LogS:	-4.454
# Rotatable Bonds:	1
TPSA:	91.67
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.374
Synthetic Accessibility Score:	4.994
Fsp3:	0.833
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.477
MDCK Permeability:	1.8836102753994055e-05
Pgp-inhibitor:	0.08
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.878

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	89.57245635986328%
Volume Distribution (VD):	0.573
Pgp-substrate:	6.706668376922607%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.828
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.809
CYP2C9-inhibitor:	0.156
CYP2C9-substrate:	0.257
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.316
CYP3A4-substrate:	0.277

ADMET: Excretion

Clearance (CL):	1.582
Half-life (T1/2):	0.106

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.211
Drug-inuced Liver Injury (DILI):	0.041
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.235
Maximum Recommended Daily Dose:	0.89
Skin Sensitization:	0.367
Carcinogencity:	0.131
Eye Corrosion:	0.403
Eye Irritation:	0.445
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC147232

Natural Product ID:	NPC147232
*Common Name:**	Fupenzic Acid
IUPAC Name:	(1R,2R,4aS,6aR,6aS,6bR,8aR,12aR,14bS)-1,11-dihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-10-oxo-3,4,5,6,6a,7,8,8a,13,14b-decahydro-2H-picene-4a-carboxylic acid
Synonyms:
Standard InCHIKey:	FMTPULGTIHBJRT-BBRBLNSOSA-N
Standard InCHI:	InChI=1S/C30H44O5/c1-17-10-13-30(24(33)34)15-14-27(5)18(22(30)29(17,7)35)8-9-21-26(4)16-19(31)23(32)25(2,3)20(26)11-12-28(21,27)6/h8,16-17,20-22,31,35H,9-15H2,1-7H3,(H,33,34)/t17-,20+,21-,22-,26+,27-,28-,29-,30+/m1/s1
SMILES:	C[C@@H]1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)C=C(C(=O)C(C)(C)[C@@H]5CC[C@@]34C)O)[C@@H]2[C@]1(C)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3114758
PubChem CID:	12045007
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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	Roots	n.a.	n.a.	PMID[24461297]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[24063567]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[21381697]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[20467822]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodcont.2014.02.001]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19774	Rubus idaeus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1524	Rosa rugosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
Others	1

Activity Type	# Activity
Individual Protein	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT462	Individual Protein	Sucrase-isomaltase	Rattus norvegicus	Inhibition	<	10.0	%	PMID[548267]

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☑ 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 NPC147232 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	219
0.1-0.2	1422
0.2-0.3	5258
0.3-0.4	12384
0.4-0.5	10611
0.5-0.6	6709
0.6-0.7	4712
0.7-0.8	1219
0.8-0.85	143
0.85-0.9	18
0.9-0.95	1
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9	High Similarity	NPC112454
0.8913	High Similarity	NPC263780
0.883	High Similarity	NPC62516
0.883	High Similarity	NPC157113
0.8817	High Similarity	NPC23170

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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 NPC147232 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	219
0.1-0.2	1733
0.2-0.3	3864
0.3-0.4	2179
0.4-0.5	740
0.5-0.6	181
0.6-0.7	146
0.7-0.8	82
0.8-0.85	5
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9	High Similarity	NPD7285	Clinical (unspecified phase)
0.8409	Intermediate Similarity	NPD4695	Discontinued
0.8404	Intermediate Similarity	NPD7515	Phase 2
0.8351	Intermediate Similarity	NPD7902	Approved
0.8229	Intermediate Similarity	NPD7748	Approved

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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