NPASS Compound

Structure

NPC134480 OpenBabel07101718292D 56 58 0 0 1 0 0 0 0 0999 V2000 -5.6625 -0.0401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7573 -2.3099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4225 0.9710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0501 0.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5058 -1.6511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0762 3.1977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0238 -1.5385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8337 -1.9573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6777 -0.2138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7421 -2.1362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2664 -1.0229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0349 0.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2816 -1.1965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9092 -1.7889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1218 2.6768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8515 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4689 1.5692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4073 1.1447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8479 -0.7114 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4334 3.9638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8025 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1922 1.0900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3612 -0.4305 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1066 2.8504 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8479 2.3295 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3769 1.4920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4790 3.4428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7494 2.0844 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4413 -0.4305 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3612 2.0485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8025 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4413 2.0485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1922 0.5280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0841 -1.1965 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8940 -1.6153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0676 -2.6001 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.2360 -0.6756 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.6180 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3903 0.8090 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.7342 2.2580 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.7754 4.9034 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3618 1.6656 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8210 4.3825 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 -1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0841 2.8145 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1770 0.3544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8501 -0.5537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9547 2.3295 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4486 3.7901 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5058 3.2692 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 1.9547 -0.7114 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1922 2.0485 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1.8515 0.3090 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 9 1 0 0 0 0 2 10 1 0 0 0 0 3 19 1 0 0 0 0 4 19 1 0 0 0 0 6 21 1 0 0 0 0 8 37 1 0 0 0 0 9 12 1 0 0 0 0 10 36 1 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 12 27 1 0 0 0 0 14 37 1 0 0 0 0 15 28 1 0 0 0 0 16 26 1 0 0 0 0 16 50 1 0 0 0 0 17 22 2 0 0 0 0 17 56 1 0 0 0 0 18 23 2 0 0 0 0 18 55 1 0 0 0 0 20 5 1 1 0 0 0 20 24 1 0 0 0 0 20 33 1 0 0 0 0 21 43 2 0 0 0 0 21 51 1 0 0 0 0 22 34 1 0 0 0 0 22 41 1 0 0 0 0 23 35 1 0 0 0 0 23 40 1 0 0 0 0 24 13 1 6 0 0 0 24 53 1 0 0 0 0 25 15 1 6 0 0 0 25 29 1 0 0 0 0 25 51 1 0 0 0 0 26 31 1 0 0 0 0 26 52 1 6 0 0 0 27 42 2 3 0 0 0 27 44 1 0 0 0 0 28 45 2 0 0 0 0 28 52 1 0 0 0 0 29 19 1 6 0 0 0 29 42 1 0 0 0 0 30 32 1 0 0 0 0 30 36 1 1 0 0 0 30 54 1 0 0 0 0 31 40 2 0 0 0 0 31 55 1 0 0 0 0 32 41 2 0 0 0 0 32 56 1 0 0 0 0 33 46 2 0 0 0 0 33 54 1 0 0 0 0 34 47 2 0 0 0 0 34 50 1 0 0 0 0 35 48 2 0 0 0 0 35 53 1 0 0 0 0 36 7 1 6 0 0 0 36 49 1 0 0 0 0 37 38 1 0 0 0 0 37 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	863.23
Volume:	802.387
LogP:	5.295
LogD:	2.989
LogS:	-4.237
# Rotatable Bonds:	18
TPSA:	206.61
# H-Bond Aceptor:	15
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.11
Synthetic Accessibility Score:	6.962
Fsp3:	0.676
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:	-5.084
MDCK Permeability:	2.743267577898223e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.105
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.928
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.153
Plasma Protein Binding (PPB):	99.16524505615234%
Volume Distribution (VD):	0.466
Pgp-substrate:	4.066975116729736%

ADMET: Metabolism

CYP1A2-inhibitor:	0.188
CYP1A2-substrate:	0.083
CYP2C19-inhibitor:	0.843
CYP2C19-substrate:	0.065
CYP2C9-inhibitor:	0.942
CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.038
CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.945
CYP3A4-substrate:	0.771

ADMET: Excretion

Clearance (CL):	3.564
Half-life (T1/2):	0.02

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.979
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.061
Maximum Recommended Daily Dose:	0.035
Skin Sensitization:	0.032
Carcinogencity:	0.09
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.033

Download Data

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

Natural Product: NPC134480

Natural Product ID:	NPC134480
*Common Name:**	Lyngbyabellin J
IUPAC Name:	n.a.
Synonyms:	Lyngbyabellin J
Standard InCHIKey:	PJUBBMCDPRNVHH-BQOOCNCZSA-N
Standard InCHI:	InChI=1S/C37H51Cl2N3O12S2/c1-9-12-27(44)42-29(19(3)4)25(51-21(6)43)15-28(45)52-26-16-50-34(47)22-17-56-32(41-22)30(36(7,49)10-2)54-33(46)20(5)24(13-11-14-37(8,38)39)53-35(48)23-18-55-31(26)40-23/h17-20,24-26,29-30,49H,9-16H2,1-8H3,(H,42,44)/t20-,24-,25+,26+,29-,30-,36-/m0/s1
SMILES:	CCCC(=N[C@@H](C(C)C)[C@@H](CC(=O)O[C@@H]1COC(=O)c2csc([C@@H]([C@](C)(CC)O)OC(=O)[C@@H](C)[C@H](CCCC(C)(Cl)Cl)OC(=O)c3csc1n3)n2)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1223739
PubChem CID:	46939789
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
NPO30186	Lyngbya bouillonii	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[18461997]
NPO30186	Lyngbya bouillonii	Species	Oscillatoriaceae	Bacteria	n.a.	Papua New Guinea	n.a.	PMID[20131814]
NPO30186	Lyngbya bouillonii	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20704304]

☑ 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	2

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	54.0	nM	PMID[476970]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	41.0	nM	PMID[476970]

☑ 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 NPC134480 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	192
0.1-0.2	2317
0.2-0.3	23834
0.3-0.4	14950
0.4-0.5	1241
0.5-0.6	99
0.6-0.7	52
0.7-0.8	2
0.8-0.85	0
0.85-0.9	2
0.9-0.95	5
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.9936	High Similarity	NPC473704
0.9419	High Similarity	NPC216720
0.9359	High Similarity	NPC210424
0.9202	High Similarity	NPC132662
0.8896	High Similarity	NPC164006
0.8827	High Similarity	NPC475554
0.7765	Intermediate Similarity	NPC522
0.7765	Intermediate Similarity	NPC56058
0.6707	Remote Similarity	NPC89592
0.6705	Remote Similarity	NPC475390
0.659	Remote Similarity	NPC469801
0.6554	Remote Similarity	NPC119481
0.6548	Remote Similarity	NPC74917
0.6509	Remote Similarity	NPC120917
0.6505	Remote Similarity	NPC97078
0.6505	Remote Similarity	NPC470146
0.6505	Remote Similarity	NPC101980
0.6497	Remote Similarity	NPC473398
0.6477	Remote Similarity	NPC319751
0.6468	Remote Similarity	NPC469858
0.6463	Remote Similarity	NPC51692
0.6359	Remote Similarity	NPC237219
0.6358	Remote Similarity	NPC214375
0.6324	Remote Similarity	NPC312887
0.627	Remote Similarity	NPC231110
0.6265	Remote Similarity	NPC267605
0.6264	Remote Similarity	NPC50274
0.6236	Remote Similarity	NPC190329
0.6216	Remote Similarity	NPC127775
0.6216	Remote Similarity	NPC474538
0.6201	Remote Similarity	NPC474069
0.6188	Remote Similarity	NPC82436
0.6188	Remote Similarity	NPC474103
0.6188	Remote Similarity	NPC474068
0.6188	Remote Similarity	NPC474064
0.6175	Remote Similarity	NPC474515
0.6175	Remote Similarity	NPC206724
0.6171	Remote Similarity	NPC103268
0.6162	Remote Similarity	NPC21126
0.6154	Remote Similarity	NPC475683
0.6154	Remote Similarity	NPC474102
0.6154	Remote Similarity	NPC157194
0.6154	Remote Similarity	NPC474079
0.6154	Remote Similarity	NPC474080
0.6154	Remote Similarity	NPC21449
0.612	Remote Similarity	NPC474094
0.612	Remote Similarity	NPC185665
0.612	Remote Similarity	NPC474067
0.612	Remote Similarity	NPC475737
0.6108	Remote Similarity	NPC212214
0.6108	Remote Similarity	NPC202591
0.6089	Remote Similarity	NPC165538
0.6087	Remote Similarity	NPC154873
0.6087	Remote Similarity	NPC163147
0.6087	Remote Similarity	NPC45576
0.6087	Remote Similarity	NPC252616
0.6087	Remote Similarity	NPC109498
0.6087	Remote Similarity	NPC61667
0.6087	Remote Similarity	NPC474090
0.6087	Remote Similarity	NPC32583
0.6084	Remote Similarity	NPC135558
0.6054	Remote Similarity	NPC268063
0.6054	Remote Similarity	NPC224609
0.6043	Remote Similarity	NPC52587
0.599	Remote Similarity	NPC122427
0.599	Remote Similarity	NPC329961
0.5907	Remote Similarity	NPC34319
0.5874	Remote Similarity	NPC106235
0.5874	Remote Similarity	NPC239660
0.5873	Remote Similarity	NPC315252
0.5833	Remote Similarity	NPC222391
0.5825	Remote Similarity	NPC256912
0.5808	Remote Similarity	NPC161242
0.5806	Remote Similarity	NPC314254
0.5806	Remote Similarity	NPC313966
0.5789	Remote Similarity	NPC475196
0.575	Remote Similarity	NPC263485
0.575	Remote Similarity	NPC229160
0.575	Remote Similarity	NPC25316
0.5741	Remote Similarity	NPC145178
0.5741	Remote Similarity	NPC14877
0.5741	Remote Similarity	NPC475350
0.5729	Remote Similarity	NPC476080
0.5729	Remote Similarity	NPC201014
0.5729	Remote Similarity	NPC110129
0.5729	Remote Similarity	NPC475534
0.5714	Remote Similarity	NPC476103
0.57	Remote Similarity	NPC475330
0.5698	Remote Similarity	NPC474070
0.5672	Remote Similarity	NPC174652
0.5662	Remote Similarity	NPC251036

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 NPC134480 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	108
0.1-0.2	693
0.2-0.3	3979
0.3-0.4	3849
0.4-0.5	496
0.5-0.6	20
0.6-0.7	5
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
0.6464	Remote Similarity	NPD6915	Approved
0.6162	Remote Similarity	NPD6910	Phase 3
0.6158	Remote Similarity	NPD6916	Clinical (unspecified phase)
0.6145	Remote Similarity	NPD9579	Approved
0.612	Remote Similarity	NPD6907	Phase 2
0.6075	Remote Similarity	NPD6911	Discontinued
0.5874	Remote Similarity	NPD8339	Clinical (unspecified phase)
0.57	Remote Similarity	NPD2957	Phase 2
0.5663	Remote Similarity	NPD7916	Approved
0.5663	Remote Similarity	NPD7915	Approved

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