NPASS Compound

Structure

NPC23077 OpenBabel06302215512D 31 34 0 0 1 0 0 0 0 0999 V2000 0.8489 -7.3198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0037 -6.8322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0035 -5.8565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8483 -5.3684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8480 -4.3928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6929 -3.9047 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5380 -4.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6926 -2.9290 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5371 -2.4404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5368 -1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0003 -0.9767 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8454 -1.4653 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8452 -2.4414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0008 -2.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8466 -2.4409 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8469 -3.4409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6915 -0.9772 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6912 -1.9772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5366 -1.4658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3820 -0.9777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3823 -0.0010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5372 0.4876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6917 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8460 0.4881 0.0000 C 0 0 0 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 0.8659 0.5003 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2485 0.4987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 -5.3689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8419 -4.3932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6865 -5.8570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 29 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 16 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 16 1 0 0 0 0 12 13 1 0 0 0 0 12 26 1 0 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 18 24 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 28 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 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 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.37
Volume:	488.222
LogP:	6.083
LogD:	5.514
LogS:	-5.45
# Rotatable Bonds:	5
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.467
Synthetic Accessibility Score:	4.726
Fsp3:	0.862
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.656
MDCK Permeability:	1.5841096683288924e-05
Pgp-inhibitor:	0.972
Pgp-substrate:	0.823
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.898

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.496
Plasma Protein Binding (PPB):	97.94320678710938%
Volume Distribution (VD):	1.28
Pgp-substrate:	2.3276867866516113%

ADMET: Metabolism

CYP1A2-inhibitor:	0.134
CYP1A2-substrate:	0.563
CYP2C19-inhibitor:	0.143
CYP2C19-substrate:	0.937
CYP2C9-inhibitor:	0.358
CYP2C9-substrate:	0.232
CYP2D6-inhibitor:	0.151
CYP2D6-substrate:	0.749
CYP3A4-inhibitor:	0.654
CYP3A4-substrate:	0.653

ADMET: Excretion

Clearance (CL):	8.204
Half-life (T1/2):	0.161

ADMET: Toxicity

hERG Blockers:	0.288
Human Hepatotoxicity (H-HT):	0.12
Drug-inuced Liver Injury (DILI):	0.224
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.037
Maximum Recommended Daily Dose:	0.29
Skin Sensitization:	0.605
Carcinogencity:	0.107
Eye Corrosion:	0.004
Eye Irritation:	0.037
Respiratory Toxicity:	0.927

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

Natural Product: NPC23077

Natural Product ID:	NPC23077
*Common Name:**	PCCQJCRNEPTFRN-VUOJHTHYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PCCQJCRNEPTFRN-VUOJHTHYSA-N
Standard InCHI:	InChI=1S/C29H48O2/c1-7-20(18(2)3)9-8-19(4)23-10-11-24-27-25(13-15-29(23,24)6)28(5)14-12-22(30)16-21(28)17-26(27)31/h7,17-19,22-27,30-31H,8-16H2,1-6H3/b20-7-/t19-,22+,23-,24+,25+,26-,27+,28+,29-/m1/s1
SMILES:	C/C=C(/CC[C@@H](C)[C@H]1CC[C@H]2[C@H]3[C@H](CC[C@]12C)[C@@]1(C)CC[C@@H](CC1=C[C@H]3O)O)C(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	23659790
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3013	Clathria basilana	Species	Microcionidae	Eukaryota	n.a.	n.a.	n.a.	PMID[29094598]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Bako, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Enemore, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Gedo, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Holleta, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[24675423]
NPO13379	Schizanthus tricolor	Species	Solanaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21171571]
NPO11266	Garcinia cambogia	Species	Clusiaceae	Eukaryota	n.a.	exocarp	n.a.	PMID[21114277]
NPO13379	Schizanthus tricolor	Species	Solanaceae	Eukaryota	Aerial parts	n.a.	n.a.	PMID[20166702]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17548953]

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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC23077 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	147
0.1-0.2	1272
0.2-0.3	5591
0.3-0.4	15717
0.4-0.5	8159
0.5-0.6	5874
0.6-0.7	4206
0.7-0.8	1317
0.8-0.85	239
0.85-0.9	87
0.9-0.95	61
0.95-1	27

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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 NPC23077 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	147
0.1-0.2	1481
0.2-0.3	4219
0.3-0.4	2290
0.4-0.5	557
0.5-0.6	183
0.6-0.7	169
0.7-0.8	75
0.8-0.85	20
0.85-0.9	6
0.9-0.95	3
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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