NPASS Compound

Structure

NPC489829 OpenBabel06302216142D 64 69 0 0 1 0 0 0 0 0999 V2000 0.7981 -1.1116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5799 -0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5108 -0.8535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4309 0.5007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 0.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7225 1.8410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6478 2.8382 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.2824 3.7690 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1485 4.2690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0145 3.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8805 4.2690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7466 3.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7466 2.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8805 2.2690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0145 2.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6126 2.2690 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3410 4.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3391 5.2839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1673 5.1142 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.5917 5.9319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1915 6.7320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1378 6.4088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1229 5.4089 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1229 5.4089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0784 5.1142 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9047 4.5509 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5848 5.2839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2901 6.2395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3152 6.4620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0204 7.4176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7006 8.1506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6755 7.9281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9703 6.9725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4058 9.1062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5282 3.7690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8935 2.8382 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.9682 1.8410 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9654 1.7662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5287 2.5925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5260 2.5177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0893 3.3440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6554 4.2449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6582 4.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0949 3.4934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2187 5.0712 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7457 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6766 0.5007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2457 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.1191 -0.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9259 -1.4681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9330 -1.5875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5127 -0.6802 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6117 -1.1141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6229 -1.2631 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6340 -1.1141 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3393 -2.0696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0194 -2.8027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7331 -0.6802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.1697 -1.5064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9064 -2.0696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3942 4.2690 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2719 6.3978 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7197 1.7662 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 59 1 0 0 0 0 6 7 2 3 0 0 0 6 64 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 8 17 1 0 0 0 0 9 10 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 16 1 0 0 0 0 14 15 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 23 22 1 6 0 0 0 23 24 1 0 0 0 0 24 25 2 3 0 0 0 24 63 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 26 35 1 0 0 0 0 27 28 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 34 1 0 0 0 0 32 33 1 0 0 0 0 35 36 2 3 0 0 0 35 62 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 6 0 0 0 37 46 1 0 0 0 0 38 39 1 0 0 0 0 39 44 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 42 45 1 0 0 0 0 43 44 1 0 0 0 0 46 47 2 0 0 0 0 46 48 1 0 0 0 0 48 52 1 0 0 0 0 48 49 1 0 0 0 0 49 50 1 0 0 0 0 50 51 1 0 0 0 0 52 51 1 6 0 0 0 52 53 1 0 0 0 0 53 54 2 3 0 0 0 53 61 1 0 0 0 0 54 55 1 0 0 0 0 55 56 1 6 0 0 0 55 58 1 0 0 0 0 56 57 1 0 0 0 0 58 59 2 3 0 0 0 58 60 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	883.41
Volume:	884.32
LogP:	0.867
LogD:	2.479
LogS:	-4.236
# Rotatable Bonds:	9
TPSA:	270.53
# H-Bond Aceptor:	18
# H-Bond Donor:	9
# Rings:	6
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.147
Synthetic Accessibility Score:	5.548
Fsp3:	0.457
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:	-6.885
MDCK Permeability:	6.663389285677113e-06
Pgp-inhibitor:	0.057
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.91
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.031
Plasma Protein Binding (PPB):	56.906158447265625%
Volume Distribution (VD):	0.579
Pgp-substrate:	29.036327362060547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.003
CYP2C19-inhibitor:	0.082
CYP2C19-substrate:	0.034
CYP2C9-inhibitor:	0.341
CYP2C9-substrate:	0.957
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.218
CYP3A4-inhibitor:	0.705
CYP3A4-substrate:	0.012

ADMET: Excretion

Clearance (CL):	6.765
Half-life (T1/2):	0.886

ADMET: Toxicity

hERG Blockers:	0.059
Human Hepatotoxicity (H-HT):	0.989
Drug-inuced Liver Injury (DILI):	0.925
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.95
Maximum Recommended Daily Dose:	0.948
Skin Sensitization:	0.197
Carcinogencity:	0.358
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.357

Download Data

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

Natural Product: NPC489829

Natural Product ID:	NPC489829
*Common Name:**	STRWMLGXJXOZRE-ZTYVOHGWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	STRWMLGXJXOZRE-ZTYVOHGWSA-N
Standard InCHI:	InChI=1S/C46H57N7O11/c1-26(2)21-33-40(58)49-35(23-28-9-15-31(56)16-10-28)45(63)52-19-3-5-38(52)43(61)48-34(22-27-7-13-30(55)14-8-27)41(59)50-36(24-29-11-17-32(57)18-12-29)46(64)53-20-4-6-39(53)44(62)51-37(25-54)42(60)47-33/h7-18,26,33-39,54-57H,3-6,19-25H2,1-2H3,(H,47,60)(H,48,61)(H,49,58)(H,50,59)(H,51,62)/t33-,34-,35-,36-,37-,38-,39-/m0/s1
SMILES:	CC(C)C[C@H]1C(=N[C@@H](Cc2ccc(cc2)O)C(=O)N2CCC[C@H]2C(=N[C@@H](Cc2ccc(cc2)O)C(=N[C@@H](Cc2ccc(cc2)O)C(=O)N2CCC[C@H]2C(=N[C@@H](CO)C(=N1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	132516355
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:0004831] Oligopeptides

*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
NPO27991	Stylissa flabelliformis	Species	Axinellidae	Eukaryota	n.a.	Maldive Islands	1995	PMID[18327911]
NPO27991	Stylissa flabelliformis	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[29893558]
NPO27991	Stylissa flabelliformis	Species	Axinellidae	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	9
MIC	10

Activity Type	# Activity
Cell Line	6
Organism	10
Others	2
Protein Complex	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	>	50000.0	nM	PMID[29893558]
NPT111	Cell Line	K562	Homo sapiens	IC50	>	50000.0	nM	PMID[29893558]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	>	50000.0	nM	PMID[29893558]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	50000.0	nM	PMID[29893558]
NPT1086	Cell Line	SK-HEP1	Homo sapiens	IC50	>	50000.0	nM	PMID[29893558]
NPT2548	Cell Line	SNU-638	Homo sapiens	IC50	>	50000.0	nM	PMID[29893558]
NPT2890	Protein Complex	Sodium/potassium-transporting ATPase	Homo sapiens	IC50	>	100000.0	nM	PMID[29893558]
NPT2	Others	Unspecified		IC50	>	100000.0	nM	PMID[29893558]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	128000.0	nM	PMID[29893558]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	128000.0	nM	PMID[29893558]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	>	128000.0	nM	PMID[29893558]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	>	128000.0	nM	PMID[29893558]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	>	128000.0	nM	PMID[29893558]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	128000.0	nM	PMID[29893558]
NPT20	Organism	Candida albicans	Candida albicans	MIC	>	128000.0	nM	PMID[29893558]
NPT87	Organism	Aspergillus fumigatus	Aspergillus fumigatus	MIC	>	128000.0	nM	PMID[29893558]
NPT329	Organism	Trichophyton rubrum	Trichophyton rubrum	MIC	>	128000.0	nM	PMID[29893558]
NPT330	Organism	Trichophyton mentagrophytes	Trichophyton mentagrophytes	MIC	>	128000.0	nM	PMID[29893558]

☑ 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 NPC489829 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	198
0.1-0.2	1043
0.2-0.3	4124
0.3-0.4	12948
0.4-0.5	13291
0.5-0.6	9788
0.6-0.7	892
0.7-0.8	322
0.8-0.85	60
0.85-0.9	25
0.9-0.95	5
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

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 NPC489829 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	139
0.1-0.2	445
0.2-0.3	726
0.3-0.4	1652
0.4-0.5	3240
0.5-0.6	2429
0.6-0.7	491
0.7-0.8	27
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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