NPASS Compound

Structure

NPC24990 OpenBabel07101718322D 39 43 0 0 1 0 0 0 0 0999 V2000 3.5984 3.1659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9881 0.4783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7340 2.1771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7506 1.1772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8599 2.6627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8929 0.6630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0022 2.1485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3477 0.3107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2699 0.6972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1611 0.6343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9600 3.6378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0655 2.0150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5335 -0.1414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8195 2.5387 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0188 1.1486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5518 0.9162 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2869 1.1200 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8005 2.5150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9227 0.2500 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4019 3.5977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3048 2.7379 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8987 1.9641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4666 0.3813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9660 3.1832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4745 1.6472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1443 0.5327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5009 3.4944 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.5926 3.4932 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8127 1.4112 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9384 0.6822 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.3656 0.3023 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4806 2.2067 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.8986 1.9752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8582 -0.5388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6513 3.9114 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9043 1.9933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0658 0.0918 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.8087 2.6842 0.0000 S 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 2 37 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 7 2 0 0 0 0 6 15 2 0 0 0 0 7 15 1 0 0 0 0 8 9 1 0 0 0 0 9 37 1 0 0 0 0 10 15 1 0 0 0 0 11 20 1 0 0 0 0 11 27 1 0 0 0 0 12 18 2 0 0 0 0 12 38 1 0 0 0 0 13 39 1 0 0 0 0 14 1 1 1 0 0 0 14 21 1 0 0 0 0 14 36 1 0 0 0 0 16 8 1 6 0 0 0 16 26 1 0 0 0 0 16 29 1 0 0 0 0 17 10 1 6 0 0 0 17 25 1 0 0 0 0 17 30 1 0 0 0 0 18 22 1 0 0 0 0 18 28 1 0 0 0 0 19 13 1 6 0 0 0 19 23 1 0 0 0 0 19 31 1 0 0 0 0 20 28 2 0 0 0 0 20 38 1 0 0 0 0 21 24 1 6 0 0 0 21 32 1 0 0 0 0 22 29 2 3 0 0 0 22 33 1 0 0 0 0 23 30 2 3 0 0 0 23 34 1 0 0 0 0 24 27 2 3 0 0 0 24 35 1 0 0 0 0 25 32 2 0 0 0 0 25 36 1 0 0 0 0 26 31 2 0 0 0 0 26 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	586.15
Volume:	545.774
LogP:	1.838
LogD:	3.304
LogS:	-3.083
# Rotatable Bonds:	5
TPSA:	145.23
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.352
Synthetic Accessibility Score:	6.746
Fsp3:	0.423
Lipinski Rule-of-5:	Accepted
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:	-5.529
MDCK Permeability:	1.2018550478387624e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.973
Human Intestinal Absorption (HIA):	0.028
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.227
Plasma Protein Binding (PPB):	91.2652359008789%
Volume Distribution (VD):	2.615
Pgp-substrate:	8.1427640914917%

ADMET: Metabolism

CYP1A2-inhibitor:	0.091
CYP1A2-substrate:	0.108
CYP2C19-inhibitor:	0.241
CYP2C19-substrate:	0.192
CYP2C9-inhibitor:	0.319
CYP2C9-substrate:	0.314
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.137
CYP3A4-inhibitor:	0.218
CYP3A4-substrate:	0.801

ADMET: Excretion

Clearance (CL):	2.189
Half-life (T1/2):	0.318

ADMET: Toxicity

hERG Blockers:	0.169
Human Hepatotoxicity (H-HT):	0.998
Drug-inuced Liver Injury (DILI):	0.984
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.115
Maximum Recommended Daily Dose:	0.975
Skin Sensitization:	0.114
Carcinogencity:	0.081
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.955

Download Data

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

Natural Product: NPC24990

Natural Product ID:	NPC24990
*Common Name:**	Aerucyclamide D
IUPAC Name:	n.a.
Synonyms:	Aerucyclamide D
Standard InCHIKey:	MLBROOJXUZKDHY-PKPICYNOSA-N
Standard InCHI:	InChI=1S/C26H30N6O4S3/c1-14-21-24(35)27-11-20-28-18(12-38-20)22(33)29-16(8-9-37-2)26-31-19(13-39-26)23(34)30-17(25(32-21)36-14)10-15-6-4-3-5-7-15/h3-7,12,14,16-17,19,21H,8-11,13H2,1-2H3,(H,27,35)(H,29,33)(H,30,34)/t14-,16+,17+,19+,21+/m1/s1
SMILES:	C[C@@H]1[C@H]2C(=NCc3nc(cs3)C(=N[C@@H](CCSC)C3=N[C@@H](CS3)C(=N[C@@H](Cc3ccccc3)C(=N2)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL584196
PubChem CID:	25156432
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000348] Peptides [CHEMONTID:0001995] Cyclic peptides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9842728]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9249979]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	Bloom	n.a.	n.a.	PMID[29847132]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29405714]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24868986]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24642434]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	Bloom	n.a.	n.a.	PMID[24261937]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	Water Reservoir near Kibbutz Hafetz Haim, Israel	n.a.	PMID[23718637]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	n.a.	Kibbutz Geva, Israel	n.a.	PMID[23153007]
NPO3288	Microcystis aeruginosa	Species	Microcystaceae	Bacteria	bloom material	Lake Kinneret, Israel	n.a.	PMID[22280481]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
Cell Line	1
Organism	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT839	Cell Line	L6	Rattus norvegicus	IC50	>	153000.0	nM	PMID[566058]
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	IC50	=	6300.0	nM	PMID[566058]
NPT844	Organism	Trypanosoma brucei rhodesiense	Trypanosoma brucei rhodesiense	IC50	=	50100.0	nM	PMID[566058]

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☑ 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 NPC24990 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	236
0.1-0.2	2068
0.2-0.3	14319
0.3-0.4	18733
0.4-0.5	5786
0.5-0.6	1455
0.6-0.7	73
0.7-0.8	15
0.8-0.85	2
0.85-0.9	1
0.9-0.95	8
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9259	High Similarity	NPC25316
0.9259	High Similarity	NPC263485
0.9259	High Similarity	NPC229160
0.9198	High Similarity	NPC475330
0.9141	High Similarity	NPC174652

Showing 1 to 5 of 200 entries

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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 NPC24990 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	141
0.1-0.2	545
0.2-0.3	963
0.3-0.4	2190
0.4-0.5	4351
0.5-0.6	918
0.6-0.7	39
0.7-0.8	3
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7444	Intermediate Similarity	NPD7977	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD8339	Clinical (unspecified phase)
0.7092	Intermediate Similarity	NPD8071	Approved
0.7021	Intermediate Similarity	NPD6348	Clinical (unspecified phase)
0.6897	Remote Similarity	NPD5189	Clinical (unspecified phase)

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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