NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	196.07
Volume:	191.655
LogP:	0.203
LogD:	0.166
LogS:	-1.827
# Rotatable Bonds:	2
TPSA:	52.6
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.576
Synthetic Accessibility Score:	4.18
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.777
MDCK Permeability:	2.6437142878421582e-05
Pgp-inhibitor:	0.049
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.254
30% Bioavailability (F30%):	0.251

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.993
Plasma Protein Binding (PPB):	23.457778930664062%
Volume Distribution (VD):	0.854
Pgp-substrate:	77.00292205810547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.146
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.416
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.048
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.085
CYP3A4-inhibitor:	0.033
CYP3A4-substrate:	0.365

ADMET: Excretion

Clearance (CL):	4.579
Half-life (T1/2):	0.899

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.465
Drug-inuced Liver Injury (DILI):	0.243
AMES Toxicity:	0.924
Rat Oral Acute Toxicity:	0.937
Maximum Recommended Daily Dose:	0.865
Skin Sensitization:	0.951
Carcinogencity:	0.894
Eye Corrosion:	0.032
Eye Irritation:	0.485
Respiratory Toxicity:	0.746

Download Data

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

Natural Product: NPC475699

Natural Product ID:	NPC475699
*Common Name:**	(3Ar,7Ar)-6-Oxo-2,3,3A,6,7,7A-Hexahydrobenzofuran-3A-Yl Acetate
IUPAC Name:	[(3aR,7aR)-6-oxo-2,3,7,7a-tetrahydro-1-benzofuran-3a-yl] acetate
Synonyms:
Standard InCHIKey:	PZOSJQZCHVKTQJ-ZJUUUORDSA-N
Standard InCHI:	InChI=1S/C10H12O4/c1-7(11)14-10-3-2-8(12)6-9(10)13-5-4-10/h2-3,9H,4-6H2,1H3/t9-,10+/m1/s1
SMILES:	CC(=O)O[C@]12CCO[C@@H]2CC(=O)C=C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL512024
PubChem CID:	44567067
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000301] Benzofurans

*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
NPO33459	cornus controversa	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3236014]

☑ 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

Activity Type	# Activity
IC50	2

Activity Type	# Activity
Cell Line	1
NON-MOLECULAR	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	IC50	=	0.5	ug.mL-1	PMID[471278]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	4.1	ug.mL-1	PMID[471278]

☑ 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 NPC475699 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	187
0.1-0.2	1378
0.2-0.3	6220
0.3-0.4	14687
0.4-0.5	11637
0.5-0.6	5865
0.6-0.7	2279
0.7-0.8	429
0.8-0.85	10
0.85-0.9	1
0.9-0.95	0
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
0.9863	High Similarity	NPC473981
0.9863	High Similarity	NPC473980
0.9474	High Similarity	NPC475690
0.8442	Intermediate Similarity	NPC474197
0.8125	Intermediate Similarity	NPC475210
0.7952	Intermediate Similarity	NPC475947
0.7949	Intermediate Similarity	NPC476355
0.7927	Intermediate Similarity	NPC275507
0.7901	Intermediate Similarity	NPC270126
0.7875	Intermediate Similarity	NPC187568
0.7875	Intermediate Similarity	NPC41780
0.7875	Intermediate Similarity	NPC474278
0.7831	Intermediate Similarity	NPC474252
0.7791	Intermediate Similarity	NPC266957
0.7791	Intermediate Similarity	NPC72513
0.7765	Intermediate Similarity	NPC155873
0.7753	Intermediate Similarity	NPC165383
0.775	Intermediate Similarity	NPC123360
0.7722	Intermediate Similarity	NPC474280
0.7722	Intermediate Similarity	NPC140287
0.7692	Intermediate Similarity	NPC163003
0.7683	Intermediate Similarity	NPC178277
0.7654	Intermediate Similarity	NPC476028
0.7654	Intermediate Similarity	NPC171204
0.7654	Intermediate Similarity	NPC141789
0.7654	Intermediate Similarity	NPC97516
0.7647	Intermediate Similarity	NPC163615
0.7647	Intermediate Similarity	NPC38569
0.764	Intermediate Similarity	NPC300312
0.764	Intermediate Similarity	NPC111114
0.764	Intermediate Similarity	NPC261607
0.7614	Intermediate Similarity	NPC78008
0.7609	Intermediate Similarity	NPC266842
0.7595	Intermediate Similarity	NPC269206
0.7595	Intermediate Similarity	NPC58956
0.7595	Intermediate Similarity	NPC295633
0.759	Intermediate Similarity	NPC281132
0.759	Intermediate Similarity	NPC223904
0.7561	Intermediate Similarity	NPC267231
0.7561	Intermediate Similarity	NPC93763
0.7561	Intermediate Similarity	NPC108816
0.7558	Intermediate Similarity	NPC470755
0.7556	Intermediate Similarity	NPC469692
0.7556	Intermediate Similarity	NPC469645
0.7532	Intermediate Similarity	NPC470256
0.7529	Intermediate Similarity	NPC170286
0.7529	Intermediate Similarity	NPC318468
0.75	Intermediate Similarity	NPC301477
0.75	Intermediate Similarity	NPC141810
0.75	Intermediate Similarity	NPC471325
0.75	Intermediate Similarity	NPC25684
0.75	Intermediate Similarity	NPC153570
0.75	Intermediate Similarity	NPC297440
0.75	Intermediate Similarity	NPC281949
0.7473	Intermediate Similarity	NPC121825
0.7473	Intermediate Similarity	NPC167219
0.7471	Intermediate Similarity	NPC478112
0.7471	Intermediate Similarity	NPC469910
0.7471	Intermediate Similarity	NPC469483
0.7471	Intermediate Similarity	NPC38576
0.7471	Intermediate Similarity	NPC279859
0.747	Intermediate Similarity	NPC472965
0.747	Intermediate Similarity	NPC63649
0.747	Intermediate Similarity	NPC264227
0.7442	Intermediate Similarity	NPC158756
0.7439	Intermediate Similarity	NPC65603
0.7439	Intermediate Similarity	NPC57744
0.7436	Intermediate Similarity	NPC476591
0.7436	Intermediate Similarity	NPC88877
0.7412	Intermediate Similarity	NPC173609
0.7412	Intermediate Similarity	NPC85772
0.7407	Intermediate Similarity	NPC155587
0.7407	Intermediate Similarity	NPC193351
0.7407	Intermediate Similarity	NPC138408
0.7407	Intermediate Similarity	NPC226669
0.7403	Intermediate Similarity	NPC194871
0.7386	Intermediate Similarity	NPC472007
0.7386	Intermediate Similarity	NPC473248
0.7381	Intermediate Similarity	NPC469920
0.7375	Intermediate Similarity	NPC472956
0.7375	Intermediate Similarity	NPC287878
0.7368	Intermediate Similarity	NPC474742
0.7356	Intermediate Similarity	NPC21471
0.7356	Intermediate Similarity	NPC177932
0.7356	Intermediate Similarity	NPC215364
0.7356	Intermediate Similarity	NPC33570
0.7356	Intermediate Similarity	NPC125290
0.7356	Intermediate Similarity	NPC473353
0.7349	Intermediate Similarity	NPC128276
0.7333	Intermediate Similarity	NPC474232
0.7333	Intermediate Similarity	NPC49342
0.7333	Intermediate Similarity	NPC473455
0.7333	Intermediate Similarity	NPC51653
0.7333	Intermediate Similarity	NPC144133
0.7333	Intermediate Similarity	NPC251385
0.7333	Intermediate Similarity	NPC179394
0.7326	Intermediate Similarity	NPC169575
0.7326	Intermediate Similarity	NPC40746
0.7326	Intermediate Similarity	NPC59097
0.7317	Intermediate Similarity	NPC235906
0.7312	Intermediate Similarity	NPC35498
0.7312	Intermediate Similarity	NPC17585
0.7303	Intermediate Similarity	NPC476803
0.7303	Intermediate Similarity	NPC475906
0.7303	Intermediate Similarity	NPC469653
0.7303	Intermediate Similarity	NPC469631
0.7303	Intermediate Similarity	NPC475819
0.7303	Intermediate Similarity	NPC119740
0.7303	Intermediate Similarity	NPC476805
0.7303	Intermediate Similarity	NPC471047
0.7303	Intermediate Similarity	NPC150063
0.7303	Intermediate Similarity	NPC469628
0.7303	Intermediate Similarity	NPC475902
0.7294	Intermediate Similarity	NPC42470
0.7294	Intermediate Similarity	NPC24417
0.7292	Intermediate Similarity	NPC149371
0.7284	Intermediate Similarity	NPC474758
0.7284	Intermediate Similarity	NPC117746
0.7284	Intermediate Similarity	NPC15499
0.7284	Intermediate Similarity	NPC294434
0.7284	Intermediate Similarity	NPC259599
0.7284	Intermediate Similarity	NPC48641
0.7283	Intermediate Similarity	NPC471147
0.7273	Intermediate Similarity	NPC472009
0.7273	Intermediate Similarity	NPC107787
0.7263	Intermediate Similarity	NPC477512
0.7262	Intermediate Similarity	NPC471299
0.7262	Intermediate Similarity	NPC98557
0.7262	Intermediate Similarity	NPC150646
0.7262	Intermediate Similarity	NPC167881
0.7262	Intermediate Similarity	NPC99651
0.7262	Intermediate Similarity	NPC617
0.7253	Intermediate Similarity	NPC74103
0.7253	Intermediate Similarity	NPC193396
0.7253	Intermediate Similarity	NPC284185
0.7253	Intermediate Similarity	NPC70595
0.7253	Intermediate Similarity	NPC32944
0.7253	Intermediate Similarity	NPC150978
0.7253	Intermediate Similarity	NPC123177
0.7241	Intermediate Similarity	NPC96259
0.7241	Intermediate Similarity	NPC115786
0.7241	Intermediate Similarity	NPC159635
0.7241	Intermediate Similarity	NPC41856
0.7241	Intermediate Similarity	NPC141193
0.7229	Intermediate Similarity	NPC476794
0.7229	Intermediate Similarity	NPC320630
0.7229	Intermediate Similarity	NPC474760
0.7229	Intermediate Similarity	NPC116177
0.7229	Intermediate Similarity	NPC470240
0.7229	Intermediate Similarity	NPC7563
0.7222	Intermediate Similarity	NPC87306
0.7216	Intermediate Similarity	NPC475871
0.7216	Intermediate Similarity	NPC475945
0.7215	Intermediate Similarity	NPC199557
0.7209	Intermediate Similarity	NPC229825
0.7209	Intermediate Similarity	NPC26624
0.7204	Intermediate Similarity	NPC475659
0.7204	Intermediate Similarity	NPC214694
0.7204	Intermediate Similarity	NPC471142
0.7204	Intermediate Similarity	NPC477922
0.7195	Intermediate Similarity	NPC161038
0.7191	Intermediate Similarity	NPC231889
0.7191	Intermediate Similarity	NPC300779
0.7191	Intermediate Similarity	NPC160138
0.7191	Intermediate Similarity	NPC23622
0.7188	Intermediate Similarity	NPC47880
0.7188	Intermediate Similarity	NPC133907
0.7188	Intermediate Similarity	NPC110443
0.7188	Intermediate Similarity	NPC164598
0.7188	Intermediate Similarity	NPC128733
0.7188	Intermediate Similarity	NPC474339
0.7188	Intermediate Similarity	NPC185141
0.7188	Intermediate Similarity	NPC46998
0.7179	Intermediate Similarity	NPC203335
0.7176	Intermediate Similarity	NPC302426
0.7174	Intermediate Similarity	NPC288240
0.7174	Intermediate Similarity	NPC273579
0.7174	Intermediate Similarity	NPC295204
0.7174	Intermediate Similarity	NPC162205
0.7159	Intermediate Similarity	NPC319795
0.7159	Intermediate Similarity	NPC78089
0.7159	Intermediate Similarity	NPC281172
0.7159	Intermediate Similarity	NPC21469
0.7159	Intermediate Similarity	NPC261380
0.7159	Intermediate Similarity	NPC38468
0.7159	Intermediate Similarity	NPC50362
0.7159	Intermediate Similarity	NPC11804
0.7159	Intermediate Similarity	NPC165162
0.7158	Intermediate Similarity	NPC208233
0.7158	Intermediate Similarity	NPC471144
0.7143	Intermediate Similarity	NPC305157
0.7143	Intermediate Similarity	NPC471465
0.7143	Intermediate Similarity	NPC472960
0.7143	Intermediate Similarity	NPC62815
0.7143	Intermediate Similarity	NPC307846
0.7143	Intermediate Similarity	NPC475855
0.7143	Intermediate Similarity	NPC196653
0.7143	Intermediate Similarity	NPC474917
0.7143	Intermediate Similarity	NPC473619
0.7143	Intermediate Similarity	NPC474741

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 NPC475699 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	168
0.1-0.2	1936
0.2-0.3	4045
0.3-0.4	2111
0.4-0.5	614
0.5-0.6	240
0.6-0.7	32
0.7-0.8	4
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
0.7356	Intermediate Similarity	NPD1694	Approved
0.7159	Intermediate Similarity	NPD1733	Clinical (unspecified phase)
0.7021	Intermediate Similarity	NPD1698	Clinical (unspecified phase)
0.7011	Intermediate Similarity	NPD5209	Approved
0.6957	Remote Similarity	NPD5785	Approved
0.6804	Remote Similarity	NPD4225	Approved
0.6778	Remote Similarity	NPD5363	Approved
0.6667	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6596	Remote Similarity	NPD6698	Approved
0.6596	Remote Similarity	NPD46	Approved
0.6574	Remote Similarity	NPD7115	Discovery
0.6517	Remote Similarity	NPD5369	Approved
0.65	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6489	Remote Similarity	NPD1695	Approved
0.6476	Remote Similarity	NPD6371	Approved
0.6444	Remote Similarity	NPD4269	Approved
0.6444	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6444	Remote Similarity	NPD4270	Approved
0.6404	Remote Similarity	NPD4252	Approved
0.6395	Remote Similarity	NPD8039	Approved
0.6344	Remote Similarity	NPD5786	Approved
0.63	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.625	Remote Similarity	NPD7838	Discovery
0.6224	Remote Similarity	NPD5282	Discontinued
0.6222	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6196	Remote Similarity	NPD7154	Phase 3
0.6186	Remote Similarity	NPD7983	Approved
0.6186	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.6146	Remote Similarity	NPD5370	Suspended
0.6122	Remote Similarity	NPD5778	Approved
0.6122	Remote Similarity	NPD5779	Approved
0.6067	Remote Similarity	NPD4756	Discovery
0.6044	Remote Similarity	NPD4821	Approved
0.6044	Remote Similarity	NPD4820	Approved
0.6044	Remote Similarity	NPD4819	Approved
0.6044	Remote Similarity	NPD4822	Approved
0.6	Remote Similarity	NPD4249	Approved
0.6	Remote Similarity	NPD4268	Approved
0.6	Remote Similarity	NPD4271	Approved
0.5979	Remote Similarity	NPD6101	Approved
0.5979	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5963	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.5957	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5948	Remote Similarity	NPD7642	Approved
0.5938	Remote Similarity	NPD4250	Approved
0.5938	Remote Similarity	NPD4251	Approved
0.5922	Remote Similarity	NPD6648	Approved
0.5914	Remote Similarity	NPD6435	Approved
0.5913	Remote Similarity	NPD8516	Approved
0.5913	Remote Similarity	NPD8517	Approved
0.5913	Remote Similarity	NPD8515	Approved
0.5913	Remote Similarity	NPD8513	Phase 3
0.5888	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.5872	Remote Similarity	NPD2067	Discontinued
0.5865	Remote Similarity	NPD5344	Discontinued
0.5859	Remote Similarity	NPD6411	Approved
0.5859	Remote Similarity	NPD5693	Phase 1
0.5851	Remote Similarity	NPD5362	Discontinued
0.5833	Remote Similarity	NPD6686	Approved
0.5833	Remote Similarity	NPD7146	Approved
0.5833	Remote Similarity	NPD6409	Approved
0.5833	Remote Similarity	NPD5330	Approved
0.5833	Remote Similarity	NPD7521	Approved
0.5833	Remote Similarity	NPD7334	Approved
0.5833	Remote Similarity	NPD6684	Approved
0.5833	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.5824	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.5784	Remote Similarity	NPD7839	Suspended
0.5758	Remote Similarity	NPD5207	Approved
0.5729	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5727	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD5737	Approved
0.5714	Remote Similarity	NPD6672	Approved
0.5714	Remote Similarity	NPD6903	Approved
0.57	Remote Similarity	NPD7637	Suspended
0.5699	Remote Similarity	NPD5368	Approved
0.5686	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.5686	Remote Similarity	NPD5695	Phase 3
0.5684	Remote Similarity	NPD6110	Phase 1
0.5676	Remote Similarity	NPD2181	Clinical (unspecified phase)
0.5673	Remote Similarity	NPD5696	Approved
0.5667	Remote Similarity	NPD8074	Phase 3
0.5663	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.5648	Remote Similarity	NPD6008	Approved
0.5647	Remote Similarity	NPD7331	Phase 2
0.5644	Remote Similarity	NPD6399	Phase 3
0.5636	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD6053	Discontinued
0.5625	Remote Similarity	NPD8297	Approved
0.5612	Remote Similarity	NPD3573	Approved

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