NPASS Compound

Structure

NPC216720 OpenBabel07101719252D 42 44 0 0 1 0 0 0 0 0999 V2000 -1.2694 6.2885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3320 -1.0774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8520 3.0609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0926 2.4103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9003 -0.7244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7954 -0.2787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3032 7.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0007 6.8327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0923 6.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8169 6.2549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1376 3.2010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8734 0.5077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9957 5.3267 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2849 -0.7742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2863 3.6925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8909 0.5380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 5.4190 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9258 3.2095 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7598 0.8763 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9258 2.2095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2863 1.7265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8909 4.8810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7598 4.5427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9957 0.0923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9088 3.3932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9618 0.2737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7254 6.6729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3074 7.5813 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 3.5416 6.0951 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 2.4700 2.7095 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5646 1.2770 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.0239 -1.4479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4935 5.6790 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4989 5.2164 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2694 -0.8696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2412 4.3364 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4989 0.2026 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9618 5.1453 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5646 4.1420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3909 1.3435 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 3.1376 2.2180 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 14 1 0 0 0 0 3 25 1 0 0 0 0 4 25 1 0 0 0 0 5 26 1 0 0 0 0 6 26 1 0 0 0 0 7 27 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 27 1 0 0 0 0 11 15 2 0 0 0 0 11 42 1 0 0 0 0 12 16 2 0 0 0 0 12 41 1 0 0 0 0 13 1 1 1 0 0 0 13 17 1 0 0 0 0 13 22 1 0 0 0 0 14 32 2 0 0 0 0 14 37 1 0 0 0 0 15 23 1 0 0 0 0 15 30 1 0 0 0 0 16 24 1 0 0 0 0 16 31 1 0 0 0 0 17 9 1 6 0 0 0 17 38 1 0 0 0 0 18 20 1 0 0 0 0 18 25 1 6 0 0 0 18 39 1 0 0 0 0 19 21 1 0 0 0 0 19 26 1 0 0 0 0 19 37 1 1 0 0 0 20 31 2 0 0 0 0 20 41 1 0 0 0 0 21 30 2 0 0 0 0 21 42 1 0 0 0 0 22 33 2 0 0 0 0 22 39 1 0 0 0 0 23 34 2 0 0 0 0 23 38 1 0 0 0 0 24 35 2 0 0 0 0 24 40 1 0 0 0 0 25 36 1 0 0 0 0 26 40 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	664.11
Volume:	597.333
LogP:	4.597
LogD:	2.336
LogS:	-3.749
# Rotatable Bonds:	7
TPSA:	151.21
# H-Bond Aceptor:	11
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.229
Synthetic Accessibility Score:	6.324
Fsp3:	0.63
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.95
MDCK Permeability:	2.0585952370311134e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.041
20% Bioavailability (F20%):	0.983
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.094
Plasma Protein Binding (PPB):	97.83304595947266%
Volume Distribution (VD):	0.458
Pgp-substrate:	3.2623138427734375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.186
CYP1A2-substrate:	0.126
CYP2C19-inhibitor:	0.601
CYP2C19-substrate:	0.096
CYP2C9-inhibitor:	0.912
CYP2C9-substrate:	0.097
CYP2D6-inhibitor:	0.034
CYP2D6-substrate:	0.072
CYP3A4-inhibitor:	0.799
CYP3A4-substrate:	0.824

ADMET: Excretion

Clearance (CL):	2.884
Half-life (T1/2):	0.019

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.953
Drug-inuced Liver Injury (DILI):	0.975
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.084
Skin Sensitization:	0.036
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.261

Download Data

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

Natural Product: NPC216720

Natural Product ID:	NPC216720
*Common Name:**	Hectochlorin
IUPAC Name:	n.a.
Synonyms:	Hectochlorin
Standard InCHIKey:	USXIYWCPCGVOKF-NOENWEJRSA-N
Standard InCHI:	InChI=1S/C27H34Cl2N2O9S2/c1-13-17(9-8-10-27(7,28)29)38-23(34)15-11-42-21(30-15)19(37-14(2)32)26(5,6)40-24(35)16-12-41-20(31-16)18(25(3,4)36)39-22(13)33/h11-13,17-19,36H,8-10H2,1-7H3/t13-,17-,18+,19+/m0/s1
SMILES:	CC(=O)O[C@@H]1c2scc(n2)C(=O)O[C@@H](CCCC(Cl)(Cl)C)[C@H](C)C(=O)O[C@H](c2nc(C(=O)OC1(C)C)cs2)C(O)(C)C
Synthetic Gene Cluster:	BGC0001000;
ChEMBL Identifier:	CHEMBL505302
PubChem CID:	636718
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0001961] Depsipeptides [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO7961	Bursatella leachii	Species	Aplysiidae	Eukaryota	n.a.	New Zealand	n.a.	PMID[11975522]
NPO7961	Bursatella leachii	Species	Aplysiidae	Eukaryota	n.a.	Thai sea	n.a.	PMID[15974628]
NPO7961	Bursatella leachii	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
EC50	2
ED50	2
GI50	1
IC50	2
Others	4

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	1
Organism	2
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1917	Cell Line	CA46	Homo sapiens	IC50	=	20.0	nM	PMID[548476]
NPT1917	Cell Line	CA46	Homo sapiens	Ratio IC50	=	10.0	n.a.	PMID[548476]
NPT1917	Cell Line	CA46	Homo sapiens	Activity	=	37.0	%	PMID[548476]
NPT91	Cell Line	KB	Homo sapiens	ED50	=	0.86	uM	PMID[548477]
NPT639	Cell Line	NCI-H187	Homo sapiens	ED50	=	1.2	uM	PMID[548477]
NPT27	Others	Unspecified		IC50	=	300.0	nM	PMID[548476]
NPT2	Others	Unspecified		EC50	=	20000.0	nM	PMID[548476]
NPT2	Others	Unspecified		EC50	>	60000.0	nM	PMID[548476]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI50	=	5100.0	nM	PMID[548476]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	16.0	mm	PMID[548476]
NPT20	Organism	Candida albicans	Candida albicans	IZ	=	11.0	mm	PMID[548476]

☑ 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 NPC216720 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	195
0.1-0.2	2370
0.2-0.3	24736
0.3-0.4	14679
0.4-0.5	568
0.5-0.6	87
0.6-0.7	52
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	4
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
0.9932	High Similarity	NPC210424
0.9419	High Similarity	NPC134480
0.9359	High Similarity	NPC473704
0.9119	High Similarity	NPC132662
0.8974	High Similarity	NPC475554
0.8805	High Similarity	NPC164006
0.7235	Intermediate Similarity	NPC522
0.7235	Intermediate Similarity	NPC56058
0.6647	Remote Similarity	NPC469801
0.6568	Remote Similarity	NPC475390
0.6562	Remote Similarity	NPC89592
0.6519	Remote Similarity	NPC51692
0.6512	Remote Similarity	NPC119481
0.6471	Remote Similarity	NPC190329
0.6464	Remote Similarity	NPC101980
0.6464	Remote Similarity	NPC470146
0.6464	Remote Similarity	NPC97078
0.6461	Remote Similarity	NPC312887
0.6453	Remote Similarity	NPC473398
0.6441	Remote Similarity	NPC127775
0.6433	Remote Similarity	NPC319751
0.6433	Remote Similarity	NPC474069
0.6416	Remote Similarity	NPC82436
0.6416	Remote Similarity	NPC474068
0.6416	Remote Similarity	NPC474103
0.6416	Remote Similarity	NPC474064
0.641	Remote Similarity	NPC214375
0.6404	Remote Similarity	NPC231110
0.6402	Remote Similarity	NPC74917
0.6379	Remote Similarity	NPC474080
0.6379	Remote Similarity	NPC474079
0.6379	Remote Similarity	NPC475683
0.6379	Remote Similarity	NPC21449
0.6379	Remote Similarity	NPC474102
0.6379	Remote Similarity	NPC157194
0.6364	Remote Similarity	NPC120917
0.6348	Remote Similarity	NPC474538
0.6343	Remote Similarity	NPC475737
0.6343	Remote Similarity	NPC185665
0.6343	Remote Similarity	NPC474094
0.6343	Remote Similarity	NPC474067
0.6307	Remote Similarity	NPC252616
0.6307	Remote Similarity	NPC154873
0.6307	Remote Similarity	NPC109498
0.6307	Remote Similarity	NPC45576
0.6307	Remote Similarity	NPC50274
0.6307	Remote Similarity	NPC474515
0.6307	Remote Similarity	NPC32583
0.6307	Remote Similarity	NPC474090
0.6307	Remote Similarity	NPC163147
0.6307	Remote Similarity	NPC61667
0.6307	Remote Similarity	NPC206724
0.6292	Remote Similarity	NPC21126
0.6271	Remote Similarity	NPC268063
0.6271	Remote Similarity	NPC224609
0.6236	Remote Similarity	NPC202591
0.6236	Remote Similarity	NPC212214
0.6222	Remote Similarity	NPC237219
0.6211	Remote Similarity	NPC267605
0.6167	Remote Similarity	NPC52587
0.6125	Remote Similarity	NPC135558
0.6055	Remote Similarity	NPC469858
0.6023	Remote Similarity	NPC103268
0.5936	Remote Similarity	NPC34319
0.5906	Remote Similarity	NPC474070
0.5879	Remote Similarity	NPC165538
0.586	Remote Similarity	NPC222391
0.5859	Remote Similarity	NPC122427
0.5851	Remote Similarity	NPC256912
0.5815	Remote Similarity	NPC315252
0.5779	Remote Similarity	NPC329961
0.5753	Remote Similarity	NPC201014
0.5753	Remote Similarity	NPC110129
0.56	Remote Similarity	NPC475196

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 NPC216720 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	122
0.1-0.2	855
0.2-0.3	4879
0.3-0.4	3008
0.4-0.5	268
0.5-0.6	15
0.6-0.7	3
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
0.6343	Remote Similarity	NPD6907	Phase 2
0.6292	Remote Similarity	NPD6910	Phase 3
0.6289	Remote Similarity	NPD9579	Approved
0.6201	Remote Similarity	NPD6911	Discontinued
0.6145	Remote Similarity	NPD6915	Approved
0.6108	Remote Similarity	NPD6916	Clinical (unspecified phase)

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