NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	250.16
Volume:	257.505
LogP:	1.689
LogD:	2.198
LogS:	-3.991
# Rotatable Bonds:	0
TPSA:	52.99
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.506
Synthetic Accessibility Score:	5.844
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.006
MDCK Permeability:	1.2471362424548715e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.627
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.346
Plasma Protein Binding (PPB):	61.64841842651367%
Volume Distribution (VD):	1.578
Pgp-substrate:	43.824676513671875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.298
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.811
CYP2C9-inhibitor:	0.028
CYP2C9-substrate:	0.351
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.454
CYP3A4-inhibitor:	0.047
CYP3A4-substrate:	0.224

ADMET: Excretion

Clearance (CL):	6.189
Half-life (T1/2):	0.698

ADMET: Toxicity

hERG Blockers:	0.06
Human Hepatotoxicity (H-HT):	0.34
Drug-inuced Liver Injury (DILI):	0.228
AMES Toxicity:	0.019
Rat Oral Acute Toxicity:	0.66
Maximum Recommended Daily Dose:	0.833
Skin Sensitization:	0.625
Carcinogencity:	0.057
Eye Corrosion:	0.295
Eye Irritation:	0.799
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: NPC260852

Natural Product ID:	NPC260852
*Common Name:**	Hypnophilin 1
IUPAC Name:	n.a.
Synonyms:	1-Desoxyhypnohilol; Hypnophilin 1
Standard InCHIKey:	QWVCSXCJPOOQML-GVDGIJOSSA-N
Standard InCHI:	InChI=1S/C15H22O3/c1-7-10(16)12-15(18-12)6-8-5-13(2,3)11(17)9(8)14(7,15)4/h8-12,16-17H,1,5-6H2,2-4H3/t8-,9+,10-,11-,12-,14+,15-/m1/s1
SMILES:	C=C1[C@H]([C@@H]2[C@@]3(C[C@H]4CC(C)(C)[C@@H]([C@H]4[C@]13C)O)O2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL465757
PubChem CID:	44593488
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO32883	lentinus connatus bcc 8996	Species	Lentinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16309322]
NPO24980	Lentinus crinitus	Species	Lentinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO24980	Lentinus crinitus	Species	Lentinaceae	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

Activity Type	# Activity
IC50	6

Activity Type	# Activity
Cell Line	4
NON-MOLECULAR	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1460	Cell Line	L929	Mus musculus	IC50	=	0.9	ug.mL-1	PMID[468531]
NPT639	Cell Line	NCI-H187	Homo sapiens	IC50	=	0.67	ug.mL-1	PMID[468532]
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	=	1.1	ug.mL-1	PMID[468532]
NPT91	Cell Line	KB	Homo sapiens	IC50	>	20.0	ug.mL-1	PMID[468532]
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	IC50	=	3.1	ug.mL-1	PMID[468532]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	20.0	ug.mL-1	PMID[468532]

☑ 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 NPC260852 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	264
0.1-0.2	2859
0.2-0.3	13005
0.3-0.4	13558
0.4-0.5	7926
0.5-0.6	4393
0.6-0.7	630
0.7-0.8	58
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8442	Intermediate Similarity	NPC133873
0.7865	Intermediate Similarity	NPC22376
0.7765	Intermediate Similarity	NPC80622
0.7701	Intermediate Similarity	NPC471340
0.7692	Intermediate Similarity	NPC197107
0.7527	Intermediate Similarity	NPC470187
0.75	Intermediate Similarity	NPC126969
0.7468	Intermediate Similarity	NPC469328
0.7447	Intermediate Similarity	NPC39453
0.7419	Intermediate Similarity	NPC472468
0.7416	Intermediate Similarity	NPC242016
0.7391	Intermediate Similarity	NPC299527
0.7386	Intermediate Similarity	NPC472465
0.7342	Intermediate Similarity	NPC165069
0.7317	Intermediate Similarity	NPC254845
0.7312	Intermediate Similarity	NPC472466
0.7294	Intermediate Similarity	NPC170148
0.7263	Intermediate Similarity	NPC472467
0.7262	Intermediate Similarity	NPC190859
0.7253	Intermediate Similarity	NPC145245
0.7245	Intermediate Similarity	NPC471381
0.7229	Intermediate Similarity	NPC41886
0.7216	Intermediate Similarity	NPC182811
0.7215	Intermediate Similarity	NPC199937
0.7209	Intermediate Similarity	NPC476703
0.7188	Intermediate Similarity	NPC240838
0.716	Intermediate Similarity	NPC161612
0.716	Intermediate Similarity	NPC33583
0.7158	Intermediate Similarity	NPC475488
0.7143	Intermediate Similarity	NPC45125
0.7143	Intermediate Similarity	NPC476709
0.7143	Intermediate Similarity	NPC143576
0.7143	Intermediate Similarity	NPC274458
0.7113	Intermediate Similarity	NPC98165
0.7108	Intermediate Similarity	NPC471781
0.7097	Intermediate Similarity	NPC148534
0.7093	Intermediate Similarity	NPC329626
0.7093	Intermediate Similarity	NPC472472
0.7071	Intermediate Similarity	NPC186861
0.7053	Intermediate Similarity	NPC235051
0.7041	Intermediate Similarity	NPC476057
0.7041	Intermediate Similarity	NPC347923
0.7041	Intermediate Similarity	NPC261807
0.7033	Intermediate Similarity	NPC116613
0.7021	Intermediate Similarity	NPC22918
0.7011	Intermediate Similarity	NPC471454
0.701	Intermediate Similarity	NPC30477
0.701	Intermediate Similarity	NPC220221
0.701	Intermediate Similarity	NPC473348
0.701	Intermediate Similarity	NPC472873
0.6989	Remote Similarity	NPC258501
0.6979	Remote Similarity	NPC137461
0.6979	Remote Similarity	NPC258216
0.6979	Remote Similarity	NPC98193
0.697	Remote Similarity	NPC79449
0.697	Remote Similarity	NPC474957
0.6966	Remote Similarity	NPC117137
0.6966	Remote Similarity	NPC66766
0.6962	Remote Similarity	NPC15152
0.6951	Remote Similarity	NPC308522
0.6951	Remote Similarity	NPC74885
0.6941	Remote Similarity	NPC14352
0.6941	Remote Similarity	NPC234527
0.6939	Remote Similarity	NPC103165
0.6939	Remote Similarity	NPC210717
0.6939	Remote Similarity	NPC284063
0.6932	Remote Similarity	NPC477089
0.6931	Remote Similarity	NPC200672
0.6931	Remote Similarity	NPC214714
0.6915	Remote Similarity	NPC473436
0.6914	Remote Similarity	NPC250836
0.6907	Remote Similarity	NPC473258
0.69	Remote Similarity	NPC79631
0.6897	Remote Similarity	NPC293223
0.6897	Remote Similarity	NPC310643
0.6893	Remote Similarity	NPC54737
0.6889	Remote Similarity	NPC471661
0.6882	Remote Similarity	NPC171484
0.6882	Remote Similarity	NPC477668
0.6882	Remote Similarity	NPC149018
0.6882	Remote Similarity	NPC255143
0.6875	Remote Similarity	NPC114389
0.6875	Remote Similarity	NPC474699
0.6875	Remote Similarity	NPC155215
0.6869	Remote Similarity	NPC311904
0.6869	Remote Similarity	NPC471150
0.6869	Remote Similarity	NPC86843
0.6869	Remote Similarity	NPC181151
0.6863	Remote Similarity	NPC329834
0.686	Remote Similarity	NPC309178
0.6854	Remote Similarity	NPC476701
0.6848	Remote Similarity	NPC86238
0.6832	Remote Similarity	NPC26557
0.6827	Remote Similarity	NPC469959
0.6827	Remote Similarity	NPC469957
0.6827	Remote Similarity	NPC108682
0.6827	Remote Similarity	NPC472263
0.6818	Remote Similarity	NPC186109
0.6804	Remote Similarity	NPC475788
0.6804	Remote Similarity	NPC296620
0.68	Remote Similarity	NPC309493
0.6796	Remote Similarity	NPC474464
0.6786	Remote Similarity	NPC144647
0.6782	Remote Similarity	NPC36479
0.6782	Remote Similarity	NPC313185
0.6774	Remote Similarity	NPC474349
0.6774	Remote Similarity	NPC474189
0.6771	Remote Similarity	NPC470832
0.6771	Remote Similarity	NPC216284
0.6771	Remote Similarity	NPC35809
0.6765	Remote Similarity	NPC475956
0.6765	Remote Similarity	NPC475986
0.6765	Remote Similarity	NPC252242
0.6762	Remote Similarity	NPC117604
0.6747	Remote Similarity	NPC477791
0.6742	Remote Similarity	NPC52755
0.6739	Remote Similarity	NPC477667
0.6739	Remote Similarity	NPC128246
0.6739	Remote Similarity	NPC320548
0.6739	Remote Similarity	NPC111409
0.6733	Remote Similarity	NPC471242
0.6733	Remote Similarity	NPC471247
0.6733	Remote Similarity	NPC91497
0.6731	Remote Similarity	NPC474015
0.6731	Remote Similarity	NPC265502
0.6731	Remote Similarity	NPC93026
0.6731	Remote Similarity	NPC29389
0.6731	Remote Similarity	NPC469960
0.6731	Remote Similarity	NPC44004
0.6709	Remote Similarity	NPC475968
0.6709	Remote Similarity	NPC310228
0.6709	Remote Similarity	NPC52431
0.6707	Remote Similarity	NPC300442
0.6703	Remote Similarity	NPC126248
0.6702	Remote Similarity	NPC121981
0.6701	Remote Similarity	NPC293001
0.6701	Remote Similarity	NPC57304
0.6701	Remote Similarity	NPC276298
0.6701	Remote Similarity	NPC171360
0.6701	Remote Similarity	NPC63193
0.6701	Remote Similarity	NPC35959
0.6701	Remote Similarity	NPC133888
0.6701	Remote Similarity	NPC29821
0.67	Remote Similarity	NPC470684
0.67	Remote Similarity	NPC470683
0.6699	Remote Similarity	NPC260809
0.6699	Remote Similarity	NPC475701
0.6699	Remote Similarity	NPC474783
0.6699	Remote Similarity	NPC232515
0.6698	Remote Similarity	NPC59489
0.6698	Remote Similarity	NPC128133
0.6698	Remote Similarity	NPC139838
0.6667	Remote Similarity	NPC93869
0.6667	Remote Similarity	NPC259296
0.6667	Remote Similarity	NPC144486
0.6667	Remote Similarity	NPC471659
0.6667	Remote Similarity	NPC155935
0.6667	Remote Similarity	NPC167527
0.6667	Remote Similarity	NPC98276
0.6667	Remote Similarity	NPC49783
0.6667	Remote Similarity	NPC215556
0.6667	Remote Similarity	NPC216911
0.6667	Remote Similarity	NPC6765
0.6667	Remote Similarity	NPC476228
0.6667	Remote Similarity	NPC476053
0.6667	Remote Similarity	NPC255882
0.6667	Remote Similarity	NPC305698
0.6667	Remote Similarity	NPC50435
0.6667	Remote Similarity	NPC5604
0.6667	Remote Similarity	NPC476896
0.6667	Remote Similarity	NPC471112
0.6667	Remote Similarity	NPC470168
0.6667	Remote Similarity	NPC224532
0.6667	Remote Similarity	NPC256567
0.6635	Remote Similarity	NPC471111
0.6635	Remote Similarity	NPC475331
0.6635	Remote Similarity	NPC121518
0.6635	Remote Similarity	NPC475335
0.6635	Remote Similarity	NPC103298
0.6635	Remote Similarity	NPC80809
0.6635	Remote Similarity	NPC288502
0.6635	Remote Similarity	NPC181104
0.6635	Remote Similarity	NPC201144
0.6634	Remote Similarity	NPC221615
0.6633	Remote Similarity	NPC26046
0.6633	Remote Similarity	NPC119379
0.663	Remote Similarity	NPC212340
0.6628	Remote Similarity	NPC469343
0.6627	Remote Similarity	NPC162309
0.6625	Remote Similarity	NPC162109
0.6602	Remote Similarity	NPC31085
0.6602	Remote Similarity	NPC470972
0.66	Remote Similarity	NPC169270
0.66	Remote Similarity	NPC111834
0.66	Remote Similarity	NPC306797
0.66	Remote Similarity	NPC72204
0.66	Remote Similarity	NPC292718
0.6598	Remote Similarity	NPC54065
0.6598	Remote Similarity	NPC246173
0.6598	Remote Similarity	NPC297474

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 NPC260852 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	320
0.1-0.2	3617
0.2-0.3	3835
0.3-0.4	938
0.4-0.5	323
0.5-0.6	110
0.6-0.7	7
0.7-0.8	0
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
0.6989	Remote Similarity	NPD7524	Approved
0.6848	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6739	Remote Similarity	NPD6695	Phase 3
0.6593	Remote Similarity	NPD6931	Approved
0.6593	Remote Similarity	NPD6930	Phase 2
0.6484	Remote Similarity	NPD6929	Approved
0.6458	Remote Similarity	NPD7750	Discontinued
0.6354	Remote Similarity	NPD4249	Approved
0.6333	Remote Similarity	NPD6933	Approved
0.6289	Remote Similarity	NPD4251	Approved
0.6289	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.6289	Remote Similarity	NPD4250	Approved
0.6264	Remote Similarity	NPD5776	Phase 2
0.6264	Remote Similarity	NPD6925	Approved
0.625	Remote Similarity	NPD6893	Approved
0.6237	Remote Similarity	NPD7514	Phase 3
0.62	Remote Similarity	NPD7087	Discontinued
0.6196	Remote Similarity	NPD7145	Approved
0.6182	Remote Similarity	NPD6371	Approved
0.617	Remote Similarity	NPD6902	Approved
0.617	Remote Similarity	NPD4790	Discontinued
0.6111	Remote Similarity	NPD6924	Approved
0.6111	Remote Similarity	NPD6926	Approved
0.6087	Remote Similarity	NPD6932	Approved
0.6064	Remote Similarity	NPD4819	Approved
0.6064	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6064	Remote Similarity	NPD7332	Phase 2
0.6064	Remote Similarity	NPD4822	Approved
0.6064	Remote Similarity	NPD4821	Approved
0.6064	Remote Similarity	NPD4820	Approved
0.6	Remote Similarity	NPD1695	Approved
0.6	Remote Similarity	NPD6898	Phase 1
0.5978	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.5957	Remote Similarity	NPD6683	Phase 2
0.5941	Remote Similarity	NPD7838	Discovery
0.5932	Remote Similarity	NPD8033	Approved
0.5918	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5888	Remote Similarity	NPD5344	Discontinued
0.5888	Remote Similarity	NPD4159	Approved
0.5876	Remote Similarity	NPD5331	Approved
0.5876	Remote Similarity	NPD5332	Approved
0.5876	Remote Similarity	NPD5362	Discontinued
0.5851	Remote Similarity	NPD4268	Approved
0.5851	Remote Similarity	NPD4271	Approved
0.5812	Remote Similarity	NPD7327	Approved
0.5812	Remote Similarity	NPD7328	Approved
0.5789	Remote Similarity	NPD6053	Discontinued
0.5784	Remote Similarity	NPD46	Approved
0.5784	Remote Similarity	NPD6698	Approved
0.5766	Remote Similarity	NPD6412	Phase 2
0.5766	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.5763	Remote Similarity	NPD7516	Approved
0.5729	Remote Similarity	NPD7525	Registered
0.5729	Remote Similarity	NPD7509	Discontinued
0.5729	Remote Similarity	NPD4748	Discontinued
0.5728	Remote Similarity	NPD7637	Suspended
0.5727	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.5727	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD8377	Approved
0.5714	Remote Similarity	NPD8294	Approved
0.5699	Remote Similarity	NPD6942	Approved
0.5699	Remote Similarity	NPD7339	Approved
0.5684	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.5667	Remote Similarity	NPD6923	Approved
0.5667	Remote Similarity	NPD8379	Approved
0.5667	Remote Similarity	NPD8378	Approved
0.5667	Remote Similarity	NPD6922	Approved
0.5667	Remote Similarity	NPD8335	Approved
0.5667	Remote Similarity	NPD8380	Approved
0.5667	Remote Similarity	NPD8296	Approved
0.5632	Remote Similarity	NPD371	Approved
0.5631	Remote Similarity	NPD3168	Discontinued
0.5619	Remote Similarity	NPD5282	Discontinued
0.5612	Remote Similarity	NPD6435	Approved
0.5604	Remote Similarity	NPD7143	Approved
0.5604	Remote Similarity	NPD7144	Approved
0.5603	Remote Similarity	NPD8133	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