NPASS Compound

Structure

NPC255088 OpenBabel06302215142D 31 35 0 0 1 0 0 0 0 0999 V2000 -2.5053 -3.8192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3020 -2.8642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0275 -2.2106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8242 -1.2555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8954 -0.9540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6922 0.0010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4176 0.6546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8464 0.4890 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8455 1.4655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0006 1.9536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8461 0.4882 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6925 -0.0008 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5391 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3855 -0.0013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2517 0.4984 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3853 -0.9788 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2313 -1.4673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2308 -2.4443 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3841 -2.9327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5381 -2.4443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5386 -1.4673 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6724 -1.9670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6922 -0.9783 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8461 -1.4665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 -0.9775 0.0000 C 0 0 0 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 -0.8662 -0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0966 -2.9446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1700 -1.6076 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.3733 -2.5627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5497 -0.6019 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 30 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 31 1 0 0 0 0 5 6 1 0 0 0 0 5 29 2 0 0 0 0 6 7 1 1 0 0 0 8 6 1 1 0 0 0 8 9 1 0 0 0 0 8 26 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 1 0 0 0 11 12 1 0 0 0 0 11 26 1 0 0 0 0 12 13 1 6 0 0 0 12 23 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 1 1 0 0 0 16 21 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 0 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 21 23 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 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	425.29
Volume:	459.587
LogP:	4.582
LogD:	4.271
LogS:	-4.255
# Rotatable Bonds:	2
TPSA:	70.42
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.666
Synthetic Accessibility Score:	4.687
Fsp3:	0.778
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.66
MDCK Permeability:	2.12168615689734e-05
Pgp-inhibitor:	0.794
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.915
30% Bioavailability (F30%):	0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.744
Plasma Protein Binding (PPB):	92.47727966308594%
Volume Distribution (VD):	1.261
Pgp-substrate:	5.197831630706787%

ADMET: Metabolism

CYP1A2-inhibitor:	0.138
CYP1A2-substrate:	0.726
CYP2C19-inhibitor:	0.207
CYP2C19-substrate:	0.846
CYP2C9-inhibitor:	0.374
CYP2C9-substrate:	0.268
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.395
CYP3A4-inhibitor:	0.789
CYP3A4-substrate:	0.501

ADMET: Excretion

Clearance (CL):	19.063
Half-life (T1/2):	0.218

ADMET: Toxicity

hERG Blockers:	0.813
Human Hepatotoxicity (H-HT):	0.363
Drug-inuced Liver Injury (DILI):	0.271
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.631
Maximum Recommended Daily Dose:	0.924
Skin Sensitization:	0.897
Carcinogencity:	0.535
Eye Corrosion:	0.011
Eye Irritation:	0.019
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC255088

Natural Product ID:	NPC255088
*Common Name:**	NMHCTUTYNGBHMC-FNGZKJNTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NMHCTUTYNGBHMC-FNGZKJNTSA-N
Standard InCHI:	InChI=1S/C27H39NO3/c1-15-11-24(31)25(28-14-15)16(2)19-5-6-20-18-13-23(30)22-12-17(29)7-9-27(22,4)21(18)8-10-26(19,20)3/h11,14,16-22,29,31H,5-10,12-13H2,1-4H3/t16-,17-,18-,19+,20-,21-,22+,26+,27+/m0/s1
SMILES:	Cc1cc(c([C@@H](C)[C@H]2CC[C@H]3[C@@H]4CC(=O)[C@H]5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O)nc1)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:0000258] Steroids and steroid derivatives [CHEMONTID:0003569] Pregnane steroids [CHEMONTID:0001468] Gluco/mineralocorticoids, progestogins and derivatives

*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
NPO28298	Boletinus cavipes	Species	Gyrodontaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15217273]
NPO24702	Piptadenia pervillei	Species	Fabaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[19299148]
NPO21470	Conoideocrella tenuis	Species	Clavicipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21473608]
NPO21470	Conoideocrella tenuis	Species	Clavicipitaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21473608]
NPO24185	Diospyros lotus	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20496	Caragana stenophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24185	Diospyros lotus	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23260	Fomitopsis spraguei	Species	Fomitopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20496	Caragana stenophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24185	Diospyros lotus	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23260	Fomitopsis spraguei	Species	Fomitopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24748	Choristoneura rosaceana	Species	Tortricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8515	Cenchrus setaceus	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20496	Caragana stenophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24185	Diospyros lotus	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28298	Boletinus cavipes	Species	Gyrodontaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23301	Salvia macrosiphon	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2795	Haplopappus rengifoanus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24423	Agaricus albus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24702	Piptadenia pervillei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24340	Acacia trineura	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21470	Conoideocrella tenuis	Species	Clavicipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24906	Inga reticulata	Species	Oecophoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23927	Trichopezizella barbata	Species	Hyaloscyphaceae	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 NPC255088 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	333
0.1-0.2	1499
0.2-0.3	4822
0.3-0.4	12701
0.4-0.5	17334
0.5-0.6	4257
0.6-0.7	1678
0.7-0.8	72
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
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 NPC255088 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	210
0.1-0.2	571
0.2-0.3	602
0.3-0.4	1624
0.4-0.5	3291
0.5-0.6	2277
0.6-0.7	539
0.7-0.8	36
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