NPASS Compound

Structure

CID176336 OpenBabel06191715552D 31 33 0 0 1 0 0 0 0 0999 V2000 -6.1962 6.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6962 2.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6962 5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1962 4.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6962 5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6962 3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6962 3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 4.7321 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 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 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 -6.6962 5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1962 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6962 3.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1962 4.7321 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 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 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 6 14 2 0 0 0 0 7 17 1 0 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 23 1 0 0 0 0 10 11 1 0 0 0 0 10 24 1 0 0 0 0 11 31 1 0 0 0 0 12 18 2 0 0 0 0 12 19 1 0 0 0 0 13 16 1 0 0 0 0 13 22 1 0 0 0 0 14 23 1 0 0 0 0 15 17 1 0 0 0 0 15 22 1 6 0 0 0 16 20 1 0 0 0 0 16 21 2 0 0 0 0 17 23 1 6 0 0 0 18 20 1 0 0 0 0 18 24 1 0 0 0 0 19 21 1 0 0 0 0 19 25 2 0 0 0 0 20 26 2 0 0 0 0 21 27 1 0 0 0 0 22 3 1 1 0 0 0 23 4 1 6 0 0 0 28 31 1 0 0 0 0 29 31 2 0 0 0 0 30 31 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	451.2
Volume:	449.76
LogP:	2.558
LogD:	2.378
LogS:	-2.428
# Rotatable Bonds:	5
TPSA:	127.42
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.168
Synthetic Accessibility Score:	5.009
Fsp3:	0.609
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.502
MDCK Permeability:	8.38203322928166e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.08
Human Intestinal Absorption (HIA):	0.79
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.079
Plasma Protein Binding (PPB):	98.75191497802734%
Volume Distribution (VD):	0.451
Pgp-substrate:	2.8160555362701416%

ADMET: Metabolism

CYP1A2-inhibitor:	0.038
CYP1A2-substrate:	0.709
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.492
CYP2C9-inhibitor:	0.136
CYP2C9-substrate:	0.603
CYP2D6-inhibitor:	0.087
CYP2D6-substrate:	0.192
CYP3A4-inhibitor:	0.209
CYP3A4-substrate:	0.161

ADMET: Excretion

Clearance (CL):	4.676
Half-life (T1/2):	0.41

ADMET: Toxicity

hERG Blockers:	0.021
Human Hepatotoxicity (H-HT):	0.372
Drug-inuced Liver Injury (DILI):	0.047
AMES Toxicity:	0.145
Rat Oral Acute Toxicity:	0.204
Maximum Recommended Daily Dose:	0.088
Skin Sensitization:	0.948
Carcinogencity:	0.802
Eye Corrosion:	0.025
Eye Irritation:	0.777
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC176336

Natural Product ID:	NPC176336
*Common Name:**	Dysidine
IUPAC Name:	n.a.
Synonyms:	Dysidine
Standard InCHIKey:	HHKUTKBQEPDLMV-CIVZFWGOSA-N
Standard InCHI:	InChI=1S/C23H33NO6S/c1-14-6-5-7-17-15(2)22(3,8-9-23(14,17)4)13-16-20(26)18(12-19(25)21(16)27)24-10-11-31(28,29)30/h6,12,15,17,24,27H,5,7-11,13H2,1-4H3,(H,28,29,30)/t15-,17+,22-,23-/m1/s1
SMILES:	CC1=CCC[C@H]2[C@@H](C)[C@](C)(CC[C@]12C)CC1=C(C(=O)C=C(C1=O)NCCS(=O)(=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL517216
PubChem CID:	NA
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0002802] Prenylquinones

*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
NPO30670	Dysidea	Genus	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11374954]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11374954]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921404]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[1593283]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18198840]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	at 1020 m depth from Chuuk Atoll, Federated States of Micronesia	n.a.	PMID[18824352]
NPO26203	Dysidea villosa	Species	Dysideidae	Eukaryota	n.a.	Hainan, China	n.a.	PMID[19091557]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20230038]
NPO30670	Dysidea	Genus	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21214221]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26551342]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26863083]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[27336796]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[32243140]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	Indo-Pacific	n.a.	PMID[7494145]
NPO30670	Dysidea	Genus	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9392880]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9748373]
NPO26203	Dysidea villosa	Species	Dysideidae	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	3
Others	8

Activity Type	# Activity
Cell Line	1
Individual Protein	6
Others	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2586	Individual Protein	Phospholipase A2, acidic	Naja naja	Inhibition	=	0.7	%	PMID[551067]
NPT2945	Individual Protein	Phospholipase A2 group 1B	Sus scrofa	Inhibition	=	1.2	%	PMID[551067]
NPT3172	Individual Protein	Phospholipase A2 group IIA	Homo sapiens	Inhibition	=	73.8	%	PMID[551067]
NPT3172	Individual Protein	Phospholipase A2 group IIA	Homo sapiens	IC50	=	2000.0	nM	PMID[551067]
NPT4422	Individual Protein	Phospholipase A2 (Bee)	Apis mellifera	Inhibition	=	33.4	%	PMID[551067]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	6700.0	nM	PMID[551068]
NPT520	Cell Line	3T3-L1	Mus musculus	Activity	=	2.3	n.a.	PMID[551068]
NPT27	Others	Unspecified		Inhibition	=	0.3	%	PMID[551067]
NPT2	Others	Unspecified		Inhibition	=	44.4	%	PMID[551067]
NPT2	Others	Unspecified		Inhibition	=	90.7	%	PMID[551067]
NPT2	Others	Unspecified		IC50	=	1300.0	nM	PMID[551067]

☑ 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 NPC176336 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	84
0.1-0.2	1017
0.2-0.3	13896
0.3-0.4	19968
0.4-0.5	6886
0.5-0.6	785
0.6-0.7	39
0.7-0.8	9
0.8-0.85	5
0.85-0.9	4
0.9-0.95	3
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9074	High Similarity	NPC72688
0.8857	High Similarity	NPC34193
0.8378	Intermediate Similarity	NPC24596
0.8198	Intermediate Similarity	NPC185929
0.7227	Intermediate Similarity	NPC175585
0.7154	Intermediate Similarity	NPC119326
0.7027	Intermediate Similarity	NPC236322
0.7	Intermediate Similarity	NPC476920
0.6721	Remote Similarity	NPC476919
0.6694	Remote Similarity	NPC230677
0.6612	Remote Similarity	NPC469958
0.6552	Remote Similarity	NPC476754
0.6525	Remote Similarity	NPC184033
0.6509	Remote Similarity	NPC1254
0.6507	Remote Similarity	NPC80738
0.65	Remote Similarity	NPC476922
0.6466	Remote Similarity	NPC476753
0.6466	Remote Similarity	NPC476752
0.6452	Remote Similarity	NPC476918
0.6423	Remote Similarity	NPC476926
0.6364	Remote Similarity	NPC99308
0.6364	Remote Similarity	NPC55869
0.6364	Remote Similarity	NPC474001
0.6351	Remote Similarity	NPC2672
0.633	Remote Similarity	NPC27817
0.6311	Remote Similarity	NPC152718
0.6311	Remote Similarity	NPC226509
0.6311	Remote Similarity	NPC58200
0.629	Remote Similarity	NPC476328
0.6281	Remote Similarity	NPC477964
0.6273	Remote Similarity	NPC108955
0.6261	Remote Similarity	NPC116231
0.625	Remote Similarity	NPC21667
0.6216	Remote Similarity	NPC470034
0.6216	Remote Similarity	NPC475863
0.619	Remote Similarity	NPC476276
0.6183	Remote Similarity	NPC477121
0.614	Remote Similarity	NPC8518
0.614	Remote Similarity	NPC132228
0.614	Remote Similarity	NPC182106
0.614	Remote Similarity	NPC311769
0.614	Remote Similarity	NPC263997
0.6126	Remote Similarity	NPC287063
0.6087	Remote Similarity	NPC472161
0.608	Remote Similarity	NPC476921
0.6055	Remote Similarity	NPC110725
0.6018	Remote Similarity	NPC103486
0.6015	Remote Similarity	NPC474006
0.6014	Remote Similarity	NPC96010
0.6014	Remote Similarity	NPC317654
0.6	Remote Similarity	NPC6185
0.6	Remote Similarity	NPC241512
0.6	Remote Similarity	NPC33881
0.5983	Remote Similarity	NPC259252
0.5965	Remote Similarity	NPC53733
0.5965	Remote Similarity	NPC105803
0.5946	Remote Similarity	NPC30321
0.5946	Remote Similarity	NPC189485
0.5929	Remote Similarity	NPC475833
0.5929	Remote Similarity	NPC225515
0.5917	Remote Similarity	NPC247316
0.5909	Remote Similarity	NPC92080
0.5873	Remote Similarity	NPC98765
0.5868	Remote Similarity	NPC23170
0.5862	Remote Similarity	NPC255174
0.5862	Remote Similarity	NPC474680
0.5849	Remote Similarity	NPC260474
0.5849	Remote Similarity	NPC188292
0.5841	Remote Similarity	NPC250632
0.584	Remote Similarity	NPC77703
0.582	Remote Similarity	NPC147232
0.5814	Remote Similarity	NPC220730
0.5798	Remote Similarity	NPC68148
0.5798	Remote Similarity	NPC65615
0.5798	Remote Similarity	NPC112454
0.5798	Remote Similarity	NPC249312
0.5789	Remote Similarity	NPC116797
0.5789	Remote Similarity	NPC474085
0.5789	Remote Similarity	NPC278459
0.5786	Remote Similarity	NPC473249
0.5785	Remote Similarity	NPC263780
0.5781	Remote Similarity	NPC195841
0.5781	Remote Similarity	NPC233256
0.5766	Remote Similarity	NPC112680
0.5766	Remote Similarity	NPC26504
0.5766	Remote Similarity	NPC292589
0.5758	Remote Similarity	NPC124358
0.575	Remote Similarity	NPC473056
0.5745	Remote Similarity	NPC478136
0.5739	Remote Similarity	NPC142253
0.5739	Remote Similarity	NPC3511
0.5726	Remote Similarity	NPC472162
0.5726	Remote Similarity	NPC32037
0.5726	Remote Similarity	NPC33663
0.5726	Remote Similarity	NPC474164
0.5726	Remote Similarity	NPC469993
0.5726	Remote Similarity	NPC8571
0.5702	Remote Similarity	NPC2482
0.5702	Remote Similarity	NPC470036
0.5702	Remote Similarity	NPC174167
0.5701	Remote Similarity	NPC310992
0.5701	Remote Similarity	NPC87141
0.569	Remote Similarity	NPC168188
0.569	Remote Similarity	NPC470015
0.568	Remote Similarity	NPC473364
0.568	Remote Similarity	NPC140685
0.5678	Remote Similarity	NPC472136
0.5676	Remote Similarity	NPC175079
0.5669	Remote Similarity	NPC176012
0.5664	Remote Similarity	NPC74410
0.5656	Remote Similarity	NPC211230
0.5652	Remote Similarity	NPC44963
0.5652	Remote Similarity	NPC189237
0.5652	Remote Similarity	NPC472684
0.5649	Remote Similarity	NPC274895
0.5649	Remote Similarity	NPC472192
0.5648	Remote Similarity	NPC474060
0.5648	Remote Similarity	NPC256846
0.5645	Remote Similarity	NPC247220
0.5641	Remote Similarity	NPC87552
0.5636	Remote Similarity	NPC470045
0.5636	Remote Similarity	NPC470044
0.5636	Remote Similarity	NPC303613
0.5636	Remote Similarity	NPC474228
0.563	Remote Similarity	NPC470523
0.5625	Remote Similarity	NPC180886
0.5621	Remote Similarity	NPC471674
0.5621	Remote Similarity	NPC201899
0.562	Remote Similarity	NPC475823
0.562	Remote Similarity	NPC35037
0.562	Remote Similarity	NPC474209
0.5615	Remote Similarity	NPC476756
0.5615	Remote Similarity	NPC244982
0.5614	Remote Similarity	NPC192329
0.561	Remote Similarity	NPC474882
0.561	Remote Similarity	NPC474328
0.5603	Remote Similarity	NPC472867
0.5603	Remote Similarity	NPC472239
0.56	Remote Similarity	NPC472166

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 NPC176336 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	75
0.1-0.2	512
0.2-0.3	3335
0.3-0.4	4298
0.4-0.5	845
0.5-0.6	83
0.6-0.7	2
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
0.6396	Remote Similarity	NPD3527	Clinical (unspecified phase)
0.6126	Remote Similarity	NPD4695	Discontinued
0.6119	Remote Similarity	NPD7739	Clinical (unspecified phase)
0.5956	Remote Similarity	NPD7624	Clinical (unspecified phase)
0.5956	Remote Similarity	NPD7623	Phase 3
0.5809	Remote Similarity	NPD7299	Clinical (unspecified phase)
0.5798	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.5786	Remote Similarity	NPD7746	Phase 1
0.5786	Remote Similarity	NPD7747	Phase 1
0.5678	Remote Similarity	NPD5690	Phase 2
0.5652	Remote Similarity	NPD8028	Phase 2

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