NPASS Compound

Structure

CID110958 OpenBabel06191715462D 26 30 0 0 1 0 0 0 0 0999 V2000 1.2321 2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7248 2.9074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9328 3.8855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2601 1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4190 2.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4345 5.6215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2851 5.0035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4680 2.2382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 1.5388 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3090 0.9511 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0981 4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8838 4.1945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2321 4.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6270 3.5254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5878 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8412 4.7080 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2905 5.1081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4400 5.5170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4930 4.0254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 12 1 0 0 0 0 2 4 2 0 0 0 0 2 13 1 0 0 0 0 3 16 1 0 0 0 0 4 17 1 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 7 12 2 0 0 0 0 7 18 1 0 0 0 0 8 13 2 0 0 0 0 8 19 1 0 0 0 0 9 14 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 10 25 1 0 0 0 0 11 24 1 0 0 0 0 11 26 1 0 0 0 0 14 5 1 6 0 0 0 14 15 1 0 0 0 0 15 6 1 1 0 0 0 15 20 1 0 0 0 0 16 18 2 0 0 0 0 16 23 1 0 0 0 0 17 19 2 0 0 0 0 17 24 1 0 0 0 0 18 25 1 0 0 0 0 19 26 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	354.11
Volume:	345.98
LogP:	3.702
LogD:	3.531
LogS:	-5.59
# Rotatable Bonds:	4
TPSA:	63.22
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.787
Synthetic Accessibility Score:	3.24
Fsp3:	0.35
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.968
MDCK Permeability:	3.180656494805589e-05
Pgp-inhibitor:	0.984
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.038

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.433
Plasma Protein Binding (PPB):	97.8028335571289%
Volume Distribution (VD):	1.58
Pgp-substrate:	3.5093319416046143%

ADMET: Metabolism

CYP1A2-inhibitor:	0.991
CYP1A2-substrate:	0.141
CYP2C19-inhibitor:	0.978
CYP2C19-substrate:	0.199
CYP2C9-inhibitor:	0.923
CYP2C9-substrate:	0.871
CYP2D6-inhibitor:	0.989
CYP2D6-substrate:	0.923
CYP3A4-inhibitor:	0.986
CYP3A4-substrate:	0.501

ADMET: Excretion

Clearance (CL):	18.04
Half-life (T1/2):	0.221

ADMET: Toxicity

hERG Blockers:	0.347
Human Hepatotoxicity (H-HT):	0.255
Drug-inuced Liver Injury (DILI):	0.767
AMES Toxicity:	0.145
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.634
Skin Sensitization:	0.805
Carcinogencity:	0.886
Eye Corrosion:	0.003
Eye Irritation:	0.305
Respiratory Toxicity:	0.223

Download Data

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

Natural Product: NPC110958

Natural Product ID:	NPC110958
*Common Name:**	(-)-Hinokinin
IUPAC Name:	(3S,4S)-3,4-bis(1,3-benzodioxol-5-ylmethyl)oxolan-2-one
Synonyms:
Standard InCHIKey:	DDWGQGZPYDSYEL-CABCVRRESA-N
Standard InCHI:	InChI=1S/C20H18O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,7-8,14-15H,5-6,9-11H2/t14-,15+/m1/s1
SMILES:	O=C1OC[C@H]([C@@H]1Cc1ccc2c(c1)OCO2)Cc1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL180970
PubChem CID:	11002708
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

*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
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9014350]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[32786878]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31347365]
NPO14158	Selaginella tamariscina	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31244143]
NPO13468.1	Cryptomeria japonica var. sinensis	Varieties	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30485090]
NPO14158	Selaginella tamariscina	Species	Selaginellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25559759]
NPO29798	Podocarpus imbricatus	Species	Podocarpaceae	Eukaryota	twigs and leaves	n.a.	n.a.	PMID[24953598]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	twig	n.a.	PMID[22474975]
NPO30638	Cryptomeria fortunei	Species	Cupressaceae	Eukaryota	bark	n.a.	n.a.	PMID[18549276]
NPO22821	Chamaecyparis obtusa	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16540181]

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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
IC50	6
Others	3

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	3
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	59.2	%	PMID[533387]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	18.3	%	PMID[533387]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	7860.0	nM	PMID[533386]
NPT111	Cell Line	K562	Homo sapiens	IC50	=	9070.0	nM	PMID[533386]
NPT2245	Cell Line	SiHa	Homo sapiens	IC50	=	68400.0	nM	PMID[533386]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	7680.0	nM	PMID[533386]
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	35700.0	nM	PMID[533386]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	72580.0	nM	PMID[533386]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	63.0	%	PMID[533385]

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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 NPC110958 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	346
0.1-0.2	1395
0.2-0.3	3028
0.3-0.4	8823
0.4-0.5	10672
0.5-0.6	5373
0.6-0.7	10978
0.7-0.8	1783
0.8-0.85	213
0.85-0.9	64
0.9-0.95	14
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC19890
0.9766	High Similarity	NPC205915
0.9692	High Similarity	NPC230968
0.9692	High Similarity	NPC102260
0.9549	High Similarity	NPC218092

Showing 1 to 5 of 200 entries

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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 NPC110958 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	283
0.1-0.2	872
0.2-0.3	1467
0.3-0.4	2617
0.4-0.5	2088
0.5-0.6	1197
0.6-0.7	543
0.7-0.8	74
0.8-0.85	9
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8333	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.8212	Intermediate Similarity	NPD4967	Phase 2
0.8212	Intermediate Similarity	NPD4966	Approved
0.8212	Intermediate Similarity	NPD4965	Approved
0.8125	Intermediate Similarity	NPD5283	Phase 1

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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