NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	360.05
Volume:	318.265
LogP:	3.581
LogD:	3.516
LogS:	-4.084
# Rotatable Bonds:	7
TPSA:	18.46
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.386
Synthetic Accessibility Score:	5.412
Fsp3:	0.625
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.212
MDCK Permeability:	1.525918378320057e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.03
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.919

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.451
Plasma Protein Binding (PPB):	91.91471862792969%
Volume Distribution (VD):	2.154
Pgp-substrate:	2.284315347671509%

ADMET: Metabolism

CYP1A2-inhibitor:	0.439
CYP1A2-substrate:	0.828
CYP2C19-inhibitor:	0.669
CYP2C19-substrate:	0.9
CYP2C9-inhibitor:	0.741
CYP2C9-substrate:	0.049
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.555
CYP3A4-inhibitor:	0.908
CYP3A4-substrate:	0.745

ADMET: Excretion

Clearance (CL):	6.673
Half-life (T1/2):	0.76

ADMET: Toxicity

hERG Blockers:	0.049
Human Hepatotoxicity (H-HT):	0.466
Drug-inuced Liver Injury (DILI):	0.921
AMES Toxicity:	0.18
Rat Oral Acute Toxicity:	0.561
Maximum Recommended Daily Dose:	0.476
Skin Sensitization:	0.576
Carcinogencity:	0.497
Eye Corrosion:	0.04
Eye Irritation:	0.179
Respiratory Toxicity:	0.87

Download Data

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

Natural Product: NPC477423

Natural Product ID:	NPC477423
*Common Name:**	(3Z,7S,9R,10R,11Z)-6-Chloro-7,10-epoxy-9-bromo-13-methoxy-3,11-pentadecadiene-1-yne
IUPAC Name:	(2R,3R,5S)-3-bromo-5-[(Z)-1-chlorohex-3-en-5-ynyl]-2-[(Z)-3-methoxypent-1-enyl]oxolane
Synonyms:
Standard InCHIKey:	ASFVDGVLCUHZLD-BJVDQNDISA-N
Standard InCHI:	InChI=1S/C16H22BrClO2/c1-4-6-7-8-14(18)16-11-13(17)15(20-16)10-9-12(5-2)19-3/h1,6-7,9-10,12-16H,5,8,11H2,2-3H3/b7-6-,10-9-/t12?,13-,14?,15-,16+/m1/s1
SMILES:	CCC(/C=C\[C@@H]1[C@@H](C[C@H](O1)C(C/C=C\C#C)Cl)Br)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25227560
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001967] Oxolanes

*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
NPO26797	Laurencia glandulifera	Species	Rhodomelaceae	Eukaryota	n.a.	the island of Crete in the south Aegean Sea	n.a.	PMID[19138151]
NPO26797	Laurencia glandulifera	Species	Rhodomelaceae	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
NPT139	Cell Line	HT-29	Homo sapiens	IC50	>=	10000	nM	PMID[19138151]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>=	10000	nM	PMID[19138151]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	>=	10000	nM	PMID[19138151]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>=	10000	nM	PMID[19138151]
NPT762	Cell Line	A-431	Homo sapiens	IC50	>=	10000	nM	PMID[19138151]

☑ 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 NPC477423 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	204
0.1-0.2	4376
0.2-0.3	22979
0.3-0.4	11275
0.4-0.5	3526
0.5-0.6	315
0.6-0.7	7
0.7-0.8	12
0.8-0.85	0
0.85-0.9	0
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9104	High Similarity	NPC477431
0.8108	Intermediate Similarity	NPC52781
0.7945	Intermediate Similarity	NPC473306
0.7867	Intermediate Similarity	NPC477421
0.7733	Intermediate Similarity	NPC477422
0.7568	Intermediate Similarity	NPC323677
0.7568	Intermediate Similarity	NPC477429
0.747	Intermediate Similarity	NPC477428
0.7432	Intermediate Similarity	NPC316572
0.7353	Intermediate Similarity	NPC26310
0.7333	Intermediate Similarity	NPC325098
0.7042	Intermediate Similarity	NPC477430
0.6757	Remote Similarity	NPC271000
0.6667	Remote Similarity	NPC474267
0.6625	Remote Similarity	NPC77724
0.6575	Remote Similarity	NPC477424
0.6316	Remote Similarity	NPC471460
0.625	Remote Similarity	NPC473453
0.6197	Remote Similarity	NPC49059
0.6197	Remote Similarity	NPC256209
0.6164	Remote Similarity	NPC471279
0.6164	Remote Similarity	NPC471277
0.6133	Remote Similarity	NPC299730
0.6111	Remote Similarity	NPC477725
0.6111	Remote Similarity	NPC477726
0.6081	Remote Similarity	NPC23418
0.6053	Remote Similarity	NPC271282
0.6053	Remote Similarity	NPC66460
0.6053	Remote Similarity	NPC325929
0.6047	Remote Similarity	NPC473947
0.6027	Remote Similarity	NPC475384
0.6027	Remote Similarity	NPC471960
0.6027	Remote Similarity	NPC473847
0.6027	Remote Similarity	NPC161838
0.6027	Remote Similarity	NPC470968
0.6027	Remote Similarity	NPC477661
0.6027	Remote Similarity	NPC470967
0.6027	Remote Similarity	NPC470966
0.6027	Remote Similarity	NPC470969
0.6	Remote Similarity	NPC83838
0.6	Remote Similarity	NPC143810
0.6	Remote Similarity	NPC469570
0.6	Remote Similarity	NPC48210
0.5976	Remote Similarity	NPC186531
0.5974	Remote Similarity	NPC29697
0.5946	Remote Similarity	NPC470970
0.5921	Remote Similarity	NPC226872
0.5921	Remote Similarity	NPC252851
0.5921	Remote Similarity	NPC471278
0.5921	Remote Similarity	NPC158368
0.5921	Remote Similarity	NPC154908
0.5897	Remote Similarity	NPC477457
0.5897	Remote Similarity	NPC477456
0.589	Remote Similarity	NPC473896
0.589	Remote Similarity	NPC473735
0.589	Remote Similarity	NPC475353
0.589	Remote Similarity	NPC473910
0.589	Remote Similarity	NPC473721
0.589	Remote Similarity	NPC473725
0.5862	Remote Similarity	NPC477088
0.5857	Remote Similarity	NPC475071
0.5843	Remote Similarity	NPC215175
0.5833	Remote Similarity	NPC26102
0.5833	Remote Similarity	NPC187361
0.5833	Remote Similarity	NPC477724
0.5802	Remote Similarity	NPC473294
0.5802	Remote Similarity	NPC471472
0.5802	Remote Similarity	NPC218477
0.5789	Remote Similarity	NPC22897
0.5789	Remote Similarity	NPC222852
0.5789	Remote Similarity	NPC159650
0.5775	Remote Similarity	NPC129263
0.5775	Remote Similarity	NPC151782
0.5753	Remote Similarity	NPC473532
0.5753	Remote Similarity	NPC269615
0.5753	Remote Similarity	NPC110732
0.5733	Remote Similarity	NPC265551
0.5733	Remote Similarity	NPC212730
0.5714	Remote Similarity	NPC475732
0.5714	Remote Similarity	NPC31194
0.5714	Remote Similarity	NPC471280
0.5714	Remote Similarity	NPC248884
0.5714	Remote Similarity	NPC471276
0.5714	Remote Similarity	NPC125122
0.5714	Remote Similarity	NPC127824
0.5714	Remote Similarity	NPC207815
0.5714	Remote Similarity	NPC85079
0.5714	Remote Similarity	NPC471275
0.5714	Remote Similarity	NPC30915
0.5699	Remote Similarity	NPC280810
0.5694	Remote Similarity	NPC142092
0.5694	Remote Similarity	NPC106531
0.5682	Remote Similarity	NPC476603
0.5679	Remote Similarity	NPC225272
0.5679	Remote Similarity	NPC472266
0.5679	Remote Similarity	NPC473752
0.5676	Remote Similarity	NPC474913
0.5676	Remote Similarity	NPC474672
0.5663	Remote Similarity	NPC129630
0.5641	Remote Similarity	NPC475984
0.5634	Remote Similarity	NPC474642
0.5634	Remote Similarity	NPC72699
0.5634	Remote Similarity	NPC249670
0.5634	Remote Similarity	NPC473913
0.5634	Remote Similarity	NPC199286
0.5634	Remote Similarity	NPC477727
0.5634	Remote Similarity	NPC471281
0.5616	Remote Similarity	NPC34577
0.561	Remote Similarity	NPC475760

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 NPC477423 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	170
0.1-0.2	4218
0.2-0.3	3924
0.3-0.4	713
0.4-0.5	122
0.5-0.6	3
0.6-0.7	0
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
		NPD

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