NPASS Compound

Structure

NPC263802 OpenBabel07101718242D 33 36 0 0 1 0 0 0 0 0999 V2000 -4.7515 2.4328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0387 3.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4570 3.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4593 2.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1042 2.9680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4133 3.9190 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 0.8660 1.5000 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 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0605 3.3838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1261 2.7601 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8171 1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3914 4.1270 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 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 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 1 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 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 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 -4.7004 5.0780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1261 -0.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 14 1 0 0 0 0 6 7 1 0 0 0 0 6 15 1 0 0 0 0 7 17 1 0 0 0 0 8 10 1 0 0 0 0 8 18 1 0 0 0 0 9 11 1 0 0 0 0 9 21 1 0 0 0 0 10 26 1 0 0 0 0 11 25 1 0 0 0 0 12 16 1 0 0 0 0 12 19 1 0 0 0 0 13 20 1 0 0 0 0 13 27 1 0 0 0 0 14 17 1 0 0 0 0 15 3 1 1 0 0 0 15 16 1 0 0 0 0 16 25 1 6 0 0 0 17 28 1 1 0 0 0 18 23 1 0 0 0 0 18 29 1 6 0 0 0 19 24 1 0 0 0 0 19 30 2 0 0 0 0 20 22 1 0 0 0 0 20 31 1 1 0 0 0 21 26 1 6 0 0 0 21 27 1 0 0 0 0 22 23 1 0 0 0 0 22 26 1 6 0 0 0 23 32 1 6 0 0 0 24 25 1 6 0 0 0 24 27 1 0 0 0 0 25 4 1 6 0 0 0 26 5 1 6 0 0 0 27 33 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	466.33
Volume:	491.427
LogP:	2.989
LogD:	3.418
LogS:	-3.445
# Rotatable Bonds:	5
TPSA:	118.22
# H-Bond Aceptor:	6
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.425
Synthetic Accessibility Score:	5.21
Fsp3:	0.963
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.915
MDCK Permeability:	1.1738626199075952e-05
Pgp-inhibitor:	0.199
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.039
20% Bioavailability (F20%):	0.621
30% Bioavailability (F30%):	0.553

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.166
Plasma Protein Binding (PPB):	79.24349212646484%
Volume Distribution (VD):	0.731
Pgp-substrate:	11.964520454406738%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.805
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.722
CYP2C9-inhibitor:	0.029
CYP2C9-substrate:	0.12
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.122
CYP3A4-inhibitor:	0.141
CYP3A4-substrate:	0.149

ADMET: Excretion

Clearance (CL):	7.598
Half-life (T1/2):	0.354

ADMET: Toxicity

hERG Blockers:	0.053
Human Hepatotoxicity (H-HT):	0.372
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.022
Rat Oral Acute Toxicity:	0.112
Maximum Recommended Daily Dose:	0.11
Skin Sensitization:	0.215
Carcinogencity:	0.033
Eye Corrosion:	0.028
Eye Irritation:	0.019
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC263802

Natural Product ID:	NPC263802
*Common Name:**	Certonardosterol Q2
IUPAC Name:	(3S,4R,5S,6S,8S,9R,10S,13R,14R,17R)-3,4,6,8-tetrahydroxy-17-[(2R,5S)-5-hydroxy-6-methylheptan-2-yl]-10,13-dimethyl-2,3,4,5,6,7,9,11,12,14,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-15-one
Synonyms:	certonardosterol Q2
Standard InCHIKey:	HHISQTCEBVYNHD-KCOPOKGBSA-N
Standard InCHI:	InChI=1S/C27H46O6/c1-14(2)17(28)7-6-15(3)16-12-19(30)24-25(16,4)11-9-21-26(5)10-8-18(29)23(32)22(26)20(31)13-27(21,24)33/h14-18,20-24,28-29,31-33H,6-13H2,1-5H3/t15-,16-,17+,18+,20+,21-,22+,23+,24-,25-,26-,27+/m1/s1
SMILES:	CC([C@H](CC[C@H]([C@H]1CC(=O)[C@@H]2[C@]1(C)CC[C@H]1[C@@]2(O)C[C@@H]([C@@H]2[C@]1(C)CC[C@@H]([C@@H]2O)O)O)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL457825
PubChem CID:	21589761
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0001110] Tetrahydroxy bile acids, alcohols 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
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497935]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104487]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662097]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12444692]

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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
ED50	5

Activity Type	# Activity
Cell Line	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT148	Cell Line	HCT-15	Homo sapiens	ED50	=	5.82	ug ml-1	PMID[543408]
NPT574	Cell Line	XF498	Homo sapiens	ED50	=	4.1	ug ml-1	PMID[543408]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	4.2	ug ml-1	PMID[543408]
NPT146	Cell Line	SK-OV-3	Homo sapiens	ED50	=	6.85	ug ml-1	PMID[543408]
NPT81	Cell Line	A549	Homo sapiens	ED50	=	6.94	ug ml-1	PMID[543408]

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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 NPC263802 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	392
0.1-0.2	3335
0.2-0.3	8394
0.3-0.4	14387
0.4-0.5	6346
0.5-0.6	5125
0.6-0.7	3556
0.7-0.8	1001
0.8-0.85	121
0.85-0.9	26
0.9-0.95	12
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.963	High Similarity	NPC50438
0.907	High Similarity	NPC56962
0.907	High Similarity	NPC24705
0.9	High Similarity	NPC170978
0.8941	High Similarity	NPC476726

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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 NPC263802 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	421
0.1-0.2	3648
0.2-0.3	3385
0.3-0.4	1012
0.4-0.5	307
0.5-0.6	205
0.6-0.7	140
0.7-0.8	20
0.8-0.85	11
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8519	High Similarity	NPD3703	Phase 2
0.8214	Intermediate Similarity	NPD6115	Approved
0.8214	Intermediate Similarity	NPD6114	Approved
0.8214	Intermediate Similarity	NPD6118	Approved
0.8214	Intermediate Similarity	NPD6697	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