NPASS Compound

Structure

NPC474445 OpenBabel07101718222D 23 22 0 0 1 0 0 0 0 0999 V2000 -6.9282 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 3 0 0 0 0 8 10 3 0 0 0 0 9 11 1 0 0 0 0 10 12 1 0 0 0 0 11 13 3 0 0 0 0 12 14 2 0 0 0 0 13 16 1 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 15 22 1 0 0 0 0 16 18 1 0 0 0 0 19 23 1 0 0 0 0 20 23 2 0 0 0 0 21 23 2 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	402.01
Volume:	348.581
LogP:	1.711
LogD:	1.276
LogS:	-1.253
# Rotatable Bonds:	8
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.37
Synthetic Accessibility Score:	4.177
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.664
MDCK Permeability:	1.4827264749328606e-05
Pgp-inhibitor:	0.008
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.949
20% Bioavailability (F20%):	0.928
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	102.03387451171875%
Volume Distribution (VD):	1.23
Pgp-substrate:	1.6749813556671143%

ADMET: Metabolism

CYP1A2-inhibitor:	0.075
CYP1A2-substrate:	0.152
CYP2C19-inhibitor:	0.687
CYP2C19-substrate:	0.63
CYP2C9-inhibitor:	0.828
CYP2C9-substrate:	0.996
CYP2D6-inhibitor:	0.096
CYP2D6-substrate:	0.818
CYP3A4-inhibitor:	0.392
CYP3A4-substrate:	0.028

ADMET: Excretion

Clearance (CL):	1.512
Half-life (T1/2):	0.064

ADMET: Toxicity

hERG Blockers:	0.001
Human Hepatotoxicity (H-HT):	0.984
Drug-inuced Liver Injury (DILI):	0.97
AMES Toxicity:	0.92
Rat Oral Acute Toxicity:	0.976
Maximum Recommended Daily Dose:	0.974
Skin Sensitization:	0.964
Carcinogencity:	0.654
Eye Corrosion:	0.959
Eye Irritation:	0.976
Respiratory Toxicity:	0.989

Download Data

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

Natural Product: NPC474445

Natural Product ID:	NPC474445
*Common Name:**	(15E)-16-Bromohexadeca-15-En-3,5,13-Triyne-1,2-Diol 1-Sulfate
IUPAC Name:	[(E)-16-bromo-2-hydroxyhexadec-15-en-3,5,13-triynyl] hydrogen sulfate
Synonyms:
Standard InCHIKey:	JLXWOPVXQDFJGS-WYMLVPIESA-N
Standard InCHI:	InChI=1S/C16H19BrO5S/c17-14-12-10-8-6-4-2-1-3-5-7-9-11-13-16(18)15-22-23(19,20)21/h12,14,16,18H,1-6,15H2,(H,19,20,21)/b14-12+
SMILES:	Br/C=C/C#CCCCCCCC#CC#CC(COS(=O)(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL468667
PubChem CID:	10046723
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000403] Organic sulfuric acids and derivatives [CHEMONTID:0003455] Sulfuric acid esters [CHEMONTID:0001185] Sulfuric acid monoesters

*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
NPO32781	diplastrella sp.	Species	Spirastrellidae	Eukaryota	n.a.	Philippines	n.a.	PMID[12762803]

☑ 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	1

Activity Type	# Activity
Individual Protein	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	IC50	=	30.0	ug.mL-1	PMID[451194]

☑ 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 NPC474445 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	723
0.1-0.2	21063
0.2-0.3	17137
0.3-0.4	3317
0.4-0.5	301
0.5-0.6	143
0.6-0.7	5
0.7-0.8	2
0.8-0.85	2
0.85-0.9	2
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9184	High Similarity	NPC475723
0.8696	High Similarity	NPC474413
0.8696	High Similarity	NPC473539
0.8043	Intermediate Similarity	NPC473625
0.8	Intermediate Similarity	NPC475153
0.8	Intermediate Similarity	NPC57011
0.717	Intermediate Similarity	NPC473768
0.6731	Remote Similarity	NPC201948
0.6316	Remote Similarity	NPC295765
0.6296	Remote Similarity	NPC157096
0.6207	Remote Similarity	NPC475560
0.6154	Remote Similarity	NPC31121
0.614	Remote Similarity	NPC93639
0.614	Remote Similarity	NPC55383
0.6129	Remote Similarity	NPC329424
0.6122	Remote Similarity	NPC216416
0.6071	Remote Similarity	NPC31194
0.6071	Remote Similarity	NPC248884
0.6071	Remote Similarity	NPC471276
0.6071	Remote Similarity	NPC471275
0.6071	Remote Similarity	NPC85079
0.6071	Remote Similarity	NPC471280
0.6071	Remote Similarity	NPC125122
0.6	Remote Similarity	NPC19834
0.6	Remote Similarity	NPC124183
0.6	Remote Similarity	NPC35141
0.6	Remote Similarity	NPC55063
0.5965	Remote Similarity	NPC471281
0.5965	Remote Similarity	NPC477727
0.5965	Remote Similarity	NPC199286
0.5965	Remote Similarity	NPC72699
0.5926	Remote Similarity	NPC62014
0.5926	Remote Similarity	NPC101616
0.5918	Remote Similarity	NPC213767
0.5862	Remote Similarity	NPC165447
0.5862	Remote Similarity	NPC294278
0.5862	Remote Similarity	NPC197272
0.5862	Remote Similarity	NPC151782
0.5862	Remote Similarity	NPC475477
0.5862	Remote Similarity	NPC89824
0.5862	Remote Similarity	NPC9273
0.5862	Remote Similarity	NPC477723
0.5862	Remote Similarity	NPC256656
0.5862	Remote Similarity	NPC76198
0.5862	Remote Similarity	NPC170776
0.5862	Remote Similarity	NPC329608
0.5862	Remote Similarity	NPC224148
0.5862	Remote Similarity	NPC471959
0.5849	Remote Similarity	NPC149668
0.5806	Remote Similarity	NPC474577
0.5789	Remote Similarity	NPC302310
0.5789	Remote Similarity	NPC153538
0.5763	Remote Similarity	NPC473705
0.569	Remote Similarity	NPC473913
0.569	Remote Similarity	NPC474642
0.569	Remote Similarity	NPC249670
0.5667	Remote Similarity	NPC477724
0.5667	Remote Similarity	NPC187361
0.5667	Remote Similarity	NPC26102
0.5636	Remote Similarity	NPC108195

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 NPC474445 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	941
0.1-0.2	6511
0.2-0.3	1410
0.3-0.4	263
0.4-0.5	23
0.5-0.6	2
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