NPASS Compound

Structure

NPC475723 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 -9.5263 -4.5000 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 -9.5263 -3.5000 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 -10.3923 -3.0000 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 -10.3923 -2.0000 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 1 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:	406.04
Volume:	353.854
LogP:	2.7
LogD:	2.198
LogS:	-1.804
# Rotatable Bonds:	11
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.312
Synthetic Accessibility Score:	3.844
Fsp3:	0.625
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.18
MDCK Permeability:	2.32194215641357e-05
Pgp-inhibitor:	0.014
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.96
20% Bioavailability (F20%):	0.992
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	101.3456802368164%
Volume Distribution (VD):	0.932
Pgp-substrate:	1.190459966659546%

ADMET: Metabolism

CYP1A2-inhibitor:	0.029
CYP1A2-substrate:	0.195
CYP2C19-inhibitor:	0.582
CYP2C19-substrate:	0.422
CYP2C9-inhibitor:	0.761
CYP2C9-substrate:	0.988
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.33
CYP3A4-inhibitor:	0.091
CYP3A4-substrate:	0.017

ADMET: Excretion

Clearance (CL):	1.739
Half-life (T1/2):	0.1

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.882
Drug-inuced Liver Injury (DILI):	0.918
AMES Toxicity:	0.725
Rat Oral Acute Toxicity:	0.953
Maximum Recommended Daily Dose:	0.979
Skin Sensitization:	0.958
Carcinogencity:	0.539
Eye Corrosion:	0.957
Eye Irritation:	0.974
Respiratory Toxicity:	0.99

Download Data

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

Natural Product: NPC475723

Natural Product ID:	NPC475723
*Common Name:**	Diplyne C Sulfate
IUPAC Name:	[(E)-16-bromo-2-hydroxyhexadec-15-en-3,5-diynyl] hydrogen sulfate
Synonyms:	Diplyne C sulfate
Standard InCHIKey:	HZARHHWAEHHVPW-WYMLVPIESA-N
Standard InCHI:	InChI=1S/C16H23BrO5S/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,1-6,8,10,15H2,(H,19,20,21)/b14-12+
SMILES:	C(CCCCC#CC#CC(COS(=O)(=O)O)O)CCCC=CBr
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL512823
PubChem CID:	10001428
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[553472]

☑ 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 NPC475723 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	183
0.1-0.2	14507
0.2-0.3	20090
0.3-0.4	6858
0.4-0.5	797
0.5-0.6	162
0.6-0.7	92
0.7-0.8	5
0.8-0.85	0
0.85-0.9	1
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9184	High Similarity	NPC474445
0.88	High Similarity	NPC475153
0.8	Intermediate Similarity	NPC474413
0.8	Intermediate Similarity	NPC473539
0.7925	Intermediate Similarity	NPC473768
0.74	Intermediate Similarity	NPC473625
0.7347	Intermediate Similarity	NPC57011
0.7037	Intermediate Similarity	NPC157096
0.6939	Remote Similarity	NPC216416
0.6923	Remote Similarity	NPC31121
0.6842	Remote Similarity	NPC93639
0.6842	Remote Similarity	NPC55383
0.6786	Remote Similarity	NPC85079
0.6786	Remote Similarity	NPC471275
0.6786	Remote Similarity	NPC471280
0.6786	Remote Similarity	NPC125122
0.6786	Remote Similarity	NPC31194
0.6786	Remote Similarity	NPC471276
0.6786	Remote Similarity	NPC248884
0.6774	Remote Similarity	NPC329424
0.6735	Remote Similarity	NPC213767
0.6727	Remote Similarity	NPC19834
0.6727	Remote Similarity	NPC124183
0.6727	Remote Similarity	NPC35141
0.6727	Remote Similarity	NPC55063
0.6667	Remote Similarity	NPC471281
0.6667	Remote Similarity	NPC477727
0.6667	Remote Similarity	NPC101616
0.6667	Remote Similarity	NPC199286
0.6667	Remote Similarity	NPC72699
0.6604	Remote Similarity	NPC149668
0.6552	Remote Similarity	NPC197272
0.6552	Remote Similarity	NPC165447
0.6552	Remote Similarity	NPC256656
0.6552	Remote Similarity	NPC170776
0.6552	Remote Similarity	NPC224148
0.6552	Remote Similarity	NPC471959
0.6552	Remote Similarity	NPC329608
0.6552	Remote Similarity	NPC151782
0.6552	Remote Similarity	NPC9273
0.6552	Remote Similarity	NPC477723
0.6552	Remote Similarity	NPC76198
0.6552	Remote Similarity	NPC89824
0.6552	Remote Similarity	NPC294278
0.6552	Remote Similarity	NPC475477
0.6491	Remote Similarity	NPC302310
0.6491	Remote Similarity	NPC153538
0.6441	Remote Similarity	NPC473705
0.6379	Remote Similarity	NPC473913
0.6379	Remote Similarity	NPC474642
0.6379	Remote Similarity	NPC249670
0.6364	Remote Similarity	NPC108195
0.6333	Remote Similarity	NPC187361
0.6333	Remote Similarity	NPC26102
0.6333	Remote Similarity	NPC477724
0.6271	Remote Similarity	NPC29234
0.625	Remote Similarity	NPC269074
0.625	Remote Similarity	NPC201948
0.623	Remote Similarity	NPC473532
0.623	Remote Similarity	NPC256209
0.623	Remote Similarity	NPC49059
0.623	Remote Similarity	NPC48058
0.6226	Remote Similarity	NPC103236
0.6226	Remote Similarity	NPC27444
0.6226	Remote Similarity	NPC329762
0.619	Remote Similarity	NPC48968
0.619	Remote Similarity	NPC470970
0.619	Remote Similarity	NPC594
0.619	Remote Similarity	NPC474577
0.6167	Remote Similarity	NPC142092
0.6167	Remote Similarity	NPC236872
0.6129	Remote Similarity	NPC474513
0.6129	Remote Similarity	NPC473725
0.6129	Remote Similarity	NPC146551
0.6129	Remote Similarity	NPC473910
0.6129	Remote Similarity	NPC473896
0.6129	Remote Similarity	NPC477725
0.6129	Remote Similarity	NPC473721
0.6129	Remote Similarity	NPC471239
0.6129	Remote Similarity	NPC473735
0.6129	Remote Similarity	NPC475353
0.6129	Remote Similarity	NPC477726
0.6129	Remote Similarity	NPC470963
0.6102	Remote Similarity	NPC473487
0.6102	Remote Similarity	NPC475071
0.6032	Remote Similarity	NPC475384
0.6032	Remote Similarity	NPC477661
0.6032	Remote Similarity	NPC471960
0.6032	Remote Similarity	NPC470968
0.6032	Remote Similarity	NPC473847
0.6032	Remote Similarity	NPC470969
0.6032	Remote Similarity	NPC470964
0.6032	Remote Similarity	NPC311648
0.6032	Remote Similarity	NPC470966
0.6032	Remote Similarity	NPC161838
0.6032	Remote Similarity	NPC470967
0.6	Remote Similarity	NPC71053
0.6	Remote Similarity	NPC129263
0.6	Remote Similarity	NPC473866
0.6	Remote Similarity	NPC59408
0.5968	Remote Similarity	NPC110732
0.5965	Remote Similarity	NPC276825
0.5938	Remote Similarity	NPC193975
0.5938	Remote Similarity	NPC121034
0.5902	Remote Similarity	NPC295765
0.5873	Remote Similarity	NPC152668
0.5873	Remote Similarity	NPC45626
0.5873	Remote Similarity	NPC474644
0.5862	Remote Similarity	NPC180575
0.5833	Remote Similarity	NPC328784
0.5833	Remote Similarity	NPC291437
0.5821	Remote Similarity	NPC325929
0.5821	Remote Similarity	NPC66460
0.5821	Remote Similarity	NPC475984
0.5821	Remote Similarity	NPC271282
0.5818	Remote Similarity	NPC469713
0.5806	Remote Similarity	NPC34577
0.5806	Remote Similarity	NPC284224
0.5806	Remote Similarity	NPC475560
0.5781	Remote Similarity	NPC474643
0.5781	Remote Similarity	NPC473865
0.5758	Remote Similarity	NPC473652
0.5741	Remote Similarity	NPC277382
0.5741	Remote Similarity	NPC171978
0.5741	Remote Similarity	NPC306850
0.5735	Remote Similarity	NPC29697
0.5735	Remote Similarity	NPC470965
0.5714	Remote Similarity	NPC304151
0.5714	Remote Similarity	NPC249801
0.5714	Remote Similarity	NPC46248
0.5692	Remote Similarity	NPC212730
0.5692	Remote Similarity	NPC265551
0.5672	Remote Similarity	NPC471278
0.5667	Remote Similarity	NPC473551
0.566	Remote Similarity	NPC195109
0.5625	Remote Similarity	NPC474672
0.5625	Remote Similarity	NPC281590

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 NPC475723 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	255
0.1-0.2	6259
0.2-0.3	2266
0.3-0.4	331
0.4-0.5	38
0.5-0.6	1
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