NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	402.18
Volume:	386.301
LogP:	3.332
LogD:	3.038
LogS:	-3.207
# Rotatable Bonds:	8
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.417
Synthetic Accessibility Score:	4.913
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.539
MDCK Permeability:	1.43E-05
Pgp-inhibitor:	0.047
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.359
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.956
Plasma Protein Binding (PPB):	78.60%
Volume Distribution (VD):	0.915
Pgp-substrate:	19.84%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.29
CYP2C19-inhibitor:	0.057
CYP2C19-substrate:	0.759
CYP2C9-inhibitor:	0.184
CYP2C9-substrate:	0.264
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.185
CYP3A4-inhibitor:	0.82
CYP3A4-substrate:	0.407

ADMET: Excretion

Clearance (CL):	5.073
Half-life (T1/2):	0.281

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.197
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.044
Rat Oral Acute Toxicity:	0.262
Maximum Recommended Daily Dose:	0.192
Skin Sensitization:	0.126
Carcinogencity:	0.225
Eye Corrosion:	0.013
Eye Irritation:	0.093
Respiratory Toxicity:	0.855

Download Data

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

Natural Product: NPC476605

Natural Product ID:	NPC476605
*Common Name:**	2-Vinyl-4-[(1R)-2alpha-(3,4-dihydroxy-4-methylpentyl)-2-methyl-3beta-bromo-6-methylenecyclohexane-1beta-yl]-2-butanol
IUPAC Name:	5-[(1S,2R,6S)-6-bromo-2-(3-hydroxy-3-methylpent-4-enyl)-1-methyl-3-methylidenecyclohexyl]-2-methylpentane-2,3-diol
Synonyms:
Standard InCHIKey:	MCXOWUJCEYTICG-YREVAHRPSA-N
Standard InCHI:	InChI=1S/C20H35BrO3/c1-7-19(5,24)12-10-15-14(2)8-9-16(21)20(15,6)13-11-17(22)18(3,4)23/h7,15-17,22-24H,1-2,8-13H2,3-6H3/t15-,16+,17?,19?,20+/m1/s1
SMILES:	C[C@]1([C@H](CCC(=C)[C@H]1CCC(C)(C=C)O)Br)CCC(C(C)(C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	122177949
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
NPO18989	Aplysia depilans	Species	Aplysiidae	Eukaryota	n.a.	Skyros Island (GPS coordinates 3887' N, 2457' E), in the North Sporades complex of the Aegean Sea, Greece	2011-AUG	PMID[25814031]
NPO18989	Aplysia depilans	Species	Aplysiidae	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	5

Activity Type	# Activity
Cell Line	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	>	100000	nM	PMID[25814031]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	>	100000	nM	PMID[25814031]
NPT1718	Cell Line	A431	Homo sapiens	IC50	>	100000	nM	PMID[25814031]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	100000	nM	PMID[25814031]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	100000	nM	PMID[25814031]

☑ 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 NPC476605 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	169
0.1-0.2	1988
0.2-0.3	11564
0.3-0.4	14771
0.4-0.5	9048
0.5-0.6	4373
0.6-0.7	714
0.7-0.8	54
0.8-0.85	10
0.85-0.9	3
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.971	High Similarity	NPC476609
0.9577	High Similarity	NPC476606
0.9041	High Similarity	NPC476607
0.9	High Similarity	NPC476604
0.8933	High Similarity	NPC476603
0.8493	Intermediate Similarity	NPC475077
0.8182	Intermediate Similarity	NPC476608
0.8101	Intermediate Similarity	NPC113024
0.8072	Intermediate Similarity	NPC174273
0.8056	Intermediate Similarity	NPC476406
0.8	Intermediate Similarity	NPC311891
0.7975	Intermediate Similarity	NPC476610
0.7973	Intermediate Similarity	NPC9942
0.7831	Intermediate Similarity	NPC313115
0.7765	Intermediate Similarity	NPC131453
0.7765	Intermediate Similarity	NPC188896
0.7674	Intermediate Similarity	NPC239453
0.7674	Intermediate Similarity	NPC224552
0.7556	Intermediate Similarity	NPC156912
0.75	Intermediate Similarity	NPC41160
0.7468	Intermediate Similarity	NPC474946
0.7468	Intermediate Similarity	NPC35397
0.7444	Intermediate Similarity	NPC257510
0.7444	Intermediate Similarity	NPC299714
0.7407	Intermediate Similarity	NPC215307
0.7407	Intermediate Similarity	NPC83351
0.7407	Intermediate Similarity	NPC167891
0.7407	Intermediate Similarity	NPC274750
0.7403	Intermediate Similarity	NPC34834
0.7375	Intermediate Similarity	NPC265588
0.7333	Intermediate Similarity	NPC267027
0.7333	Intermediate Similarity	NPC250977
0.7308	Intermediate Similarity	NPC471268
0.7308	Intermediate Similarity	NPC471271
0.7297	Intermediate Similarity	NPC225415
0.7283	Intermediate Similarity	NPC92231
0.7283	Intermediate Similarity	NPC34732
0.7237	Intermediate Similarity	NPC69649
0.7237	Intermediate Similarity	NPC68703
0.7229	Intermediate Similarity	NPC474592
0.72	Intermediate Similarity	NPC258595
0.716	Intermediate Similarity	NPC315261
0.7143	Intermediate Similarity	NPC276616
0.7143	Intermediate Similarity	NPC244790
0.7143	Intermediate Similarity	NPC471238
0.7143	Intermediate Similarity	NPC245795
0.7125	Intermediate Similarity	NPC201048
0.7125	Intermediate Similarity	NPC306727
0.7125	Intermediate Similarity	NPC476366
0.7108	Intermediate Similarity	NPC233295
0.7108	Intermediate Similarity	NPC129501
0.7105	Intermediate Similarity	NPC279434
0.7089	Intermediate Similarity	NPC471272
0.7089	Intermediate Similarity	NPC242001
0.7089	Intermediate Similarity	NPC167706
0.7073	Intermediate Similarity	NPC470711
0.7073	Intermediate Similarity	NPC91594
0.7073	Intermediate Similarity	NPC470758
0.7067	Intermediate Similarity	NPC101128
0.7067	Intermediate Similarity	NPC219940
0.7067	Intermediate Similarity	NPC309300
0.7067	Intermediate Similarity	NPC68656
0.7051	Intermediate Similarity	NPC471560
0.7051	Intermediate Similarity	NPC473893
0.7051	Intermediate Similarity	NPC210323
0.7042	Intermediate Similarity	NPC39068
0.7037	Intermediate Similarity	NPC66566
0.7037	Intermediate Similarity	NPC477923
0.7037	Intermediate Similarity	NPC32832
0.7027	Intermediate Similarity	NPC475251
0.7024	Intermediate Similarity	NPC164840
0.7024	Intermediate Similarity	NPC241290
0.7024	Intermediate Similarity	NPC209944
0.7013	Intermediate Similarity	NPC114651
0.7	Intermediate Similarity	NPC130665
0.7	Intermediate Similarity	NPC68443
0.7	Intermediate Similarity	NPC472506
0.7	Intermediate Similarity	NPC471799
0.6977	Remote Similarity	NPC474634
0.6977	Remote Similarity	NPC320548
0.6977	Remote Similarity	NPC23748
0.6962	Remote Similarity	NPC145498
0.6962	Remote Similarity	NPC189745
0.6962	Remote Similarity	NPC283316
0.6951	Remote Similarity	NPC91573
0.6951	Remote Similarity	NPC63958
0.6951	Remote Similarity	NPC329626
0.6951	Remote Similarity	NPC477925
0.6951	Remote Similarity	NPC274079
0.6951	Remote Similarity	NPC470749
0.6951	Remote Similarity	NPC253190
0.6941	Remote Similarity	NPC249423
0.6941	Remote Similarity	NPC264245
0.6923	Remote Similarity	NPC2648
0.6923	Remote Similarity	NPC208999
0.6923	Remote Similarity	NPC96484
0.6914	Remote Similarity	NPC243342
0.6914	Remote Similarity	NPC329090
0.6914	Remote Similarity	NPC476736
0.6914	Remote Similarity	NPC477138
0.6914	Remote Similarity	NPC471797
0.6914	Remote Similarity	NPC27395
0.6914	Remote Similarity	NPC91858
0.6905	Remote Similarity	NPC72755
0.6905	Remote Similarity	NPC476367
0.6905	Remote Similarity	NPC31330
0.6905	Remote Similarity	NPC328714
0.6905	Remote Similarity	NPC83436
0.6883	Remote Similarity	NPC475897
0.6883	Remote Similarity	NPC149680
0.6875	Remote Similarity	NPC477792
0.6875	Remote Similarity	NPC164045
0.6867	Remote Similarity	NPC477924
0.6867	Remote Similarity	NPC130136
0.6867	Remote Similarity	NPC31037
0.686	Remote Similarity	NPC49964
0.686	Remote Similarity	NPC218616
0.686	Remote Similarity	NPC296701
0.686	Remote Similarity	NPC87489
0.686	Remote Similarity	NPC471408
0.6854	Remote Similarity	NPC109900
0.6842	Remote Similarity	NPC144650
0.6842	Remote Similarity	NPC300593
0.6842	Remote Similarity	NPC290367
0.6835	Remote Similarity	NPC474248
0.6829	Remote Similarity	NPC328104
0.6829	Remote Similarity	NPC144075
0.6829	Remote Similarity	NPC291503
0.6829	Remote Similarity	NPC319090
0.6829	Remote Similarity	NPC185536
0.6824	Remote Similarity	NPC324772
0.6824	Remote Similarity	NPC234193
0.6824	Remote Similarity	NPC287749
0.6824	Remote Similarity	NPC95124
0.6824	Remote Similarity	NPC13554
0.6824	Remote Similarity	NPC471266
0.6824	Remote Similarity	NPC96362
0.6795	Remote Similarity	NPC308522
0.6795	Remote Similarity	NPC269077
0.6795	Remote Similarity	NPC88454
0.6795	Remote Similarity	NPC253303
0.6795	Remote Similarity	NPC74885
0.6795	Remote Similarity	NPC139207
0.6795	Remote Similarity	NPC197805
0.6795	Remote Similarity	NPC101307
0.6795	Remote Similarity	NPC117607
0.6795	Remote Similarity	NPC185874
0.679	Remote Similarity	NPC474140
0.679	Remote Similarity	NPC95165
0.679	Remote Similarity	NPC182717
0.679	Remote Similarity	NPC476422
0.679	Remote Similarity	NPC329763
0.6786	Remote Similarity	NPC247783
0.6786	Remote Similarity	NPC11908
0.6786	Remote Similarity	NPC472501
0.6786	Remote Similarity	NPC137587
0.6786	Remote Similarity	NPC269543
0.6786	Remote Similarity	NPC474216
0.6786	Remote Similarity	NPC476314
0.6786	Remote Similarity	NPC472342
0.6786	Remote Similarity	NPC301707
0.6782	Remote Similarity	NPC477978
0.6782	Remote Similarity	NPC317458
0.6782	Remote Similarity	NPC49208
0.6778	Remote Similarity	NPC133588
0.6757	Remote Similarity	NPC122239
0.6757	Remote Similarity	NPC475931
0.6753	Remote Similarity	NPC60837
0.6753	Remote Similarity	NPC2728
0.6753	Remote Similarity	NPC19569
0.6753	Remote Similarity	NPC172613
0.6753	Remote Similarity	NPC300442
0.6753	Remote Similarity	NPC64123
0.6753	Remote Similarity	NPC208198
0.6753	Remote Similarity	NPC282619
0.6753	Remote Similarity	NPC11555
0.6753	Remote Similarity	NPC471200
0.6753	Remote Similarity	NPC308844
0.6747	Remote Similarity	NPC30575
0.6747	Remote Similarity	NPC167873
0.6747	Remote Similarity	NPC61080
0.6747	Remote Similarity	NPC244488
0.6747	Remote Similarity	NPC470766
0.6747	Remote Similarity	NPC310643
0.6747	Remote Similarity	NPC38141
0.6747	Remote Similarity	NPC247325
0.6747	Remote Similarity	NPC1973
0.6744	Remote Similarity	NPC5361
0.6744	Remote Similarity	NPC471270
0.6744	Remote Similarity	NPC47761
0.6744	Remote Similarity	NPC476646
0.6744	Remote Similarity	NPC320525
0.6742	Remote Similarity	NPC175145
0.6742	Remote Similarity	NPC475069
0.6709	Remote Similarity	NPC266578
0.6707	Remote Similarity	NPC469533
0.6707	Remote Similarity	NPC18819
0.6707	Remote Similarity	NPC71152
0.6707	Remote Similarity	NPC469534
0.6707	Remote Similarity	NPC78527

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 NPC476605 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	160
0.1-0.2	2709
0.2-0.3	4166
0.3-0.4	1567
0.4-0.5	398
0.5-0.6	118
0.6-0.7	32
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
0.716	Intermediate Similarity	NPD6933	Approved
0.6914	Remote Similarity	NPD6924	Approved
0.6914	Remote Similarity	NPD6926	Approved
0.6824	Remote Similarity	NPD6931	Approved
0.6824	Remote Similarity	NPD6930	Phase 2
0.6786	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.6706	Remote Similarity	NPD6929	Approved
0.6667	Remote Similarity	NPD7524	Approved
0.6628	Remote Similarity	NPD7332	Phase 2
0.6628	Remote Similarity	NPD7514	Phase 3
0.6627	Remote Similarity	NPD8264	Approved
0.6591	Remote Similarity	NPD6695	Phase 3
0.6588	Remote Similarity	NPD7145	Approved
0.6543	Remote Similarity	NPD7143	Approved
0.6543	Remote Similarity	NPD7144	Approved
0.6517	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD5776	Phase 2
0.6471	Remote Similarity	NPD6925	Approved
0.6471	Remote Similarity	NPD6932	Approved
0.6463	Remote Similarity	NPD7151	Approved
0.6463	Remote Similarity	NPD7150	Approved
0.6463	Remote Similarity	NPD7152	Approved
0.6444	Remote Similarity	NPD6893	Approved
0.6437	Remote Similarity	NPD7525	Registered
0.6437	Remote Similarity	NPD7509	Discontinued
0.6429	Remote Similarity	NPD6942	Approved
0.6429	Remote Similarity	NPD7339	Approved
0.642	Remote Similarity	NPD6923	Approved
0.642	Remote Similarity	NPD6922	Approved
0.6364	Remote Similarity	NPD6898	Phase 1
0.6364	Remote Similarity	NPD6902	Approved
0.6364	Remote Similarity	NPD368	Approved
0.6353	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.6322	Remote Similarity	NPD7645	Phase 2
0.6304	Remote Similarity	NPD7750	Discontinued
0.6136	Remote Similarity	NPD6683	Phase 2
0.6129	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.6118	Remote Similarity	NPD4784	Approved
0.6118	Remote Similarity	NPD4785	Approved
0.6071	Remote Similarity	NPD4243	Approved
0.6042	Remote Similarity	NPD7087	Discontinued
0.6	Remote Similarity	NPD342	Phase 1
0.6	Remote Similarity	NPD4732	Discontinued
0.5978	Remote Similarity	NPD4786	Approved
0.5934	Remote Similarity	NPD3667	Approved
0.5921	Remote Similarity	NPD4219	Approved
0.587	Remote Similarity	NPD4788	Approved
0.5843	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD4267	Clinical (unspecified phase)
0.5806	Remote Similarity	NPD3665	Phase 1
0.5806	Remote Similarity	NPD3666	Approved
0.5806	Remote Similarity	NPD3133	Approved
0.5778	Remote Similarity	NPD4195	Approved
0.5773	Remote Similarity	NPD7136	Phase 2
0.5745	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.5728	Remote Similarity	NPD5344	Discontinued
0.5714	Remote Similarity	NPD4748	Discontinued
0.5714	Remote Similarity	NPD4819	Approved
0.5714	Remote Similarity	NPD4822	Approved
0.5714	Remote Similarity	NPD4820	Approved
0.5714	Remote Similarity	NPD4821	Approved
0.5714	Remote Similarity	NPD6079	Approved
0.5714	Remote Similarity	NPD7637	Suspended
0.5686	Remote Similarity	NPD4225	Approved
0.5684	Remote Similarity	NPD4623	Approved
0.5684	Remote Similarity	NPD5279	Phase 3
0.5684	Remote Similarity	NPD4519	Discontinued
0.5684	Remote Similarity	NPD3618	Phase 1
0.5682	Remote Similarity	NPD4190	Phase 3
0.5682	Remote Similarity	NPD5275	Approved
0.5673	Remote Similarity	NPD7632	Discontinued
0.567	Remote Similarity	NPD5328	Approved
0.5667	Remote Similarity	NPD3671	Phase 1
0.5625	Remote Similarity	NPD1145	Discontinued

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