NPASS Compound

Natural Product: NPC605225

Natural Product ID	NPC605225
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NEGYEDYHPHMHGK-MRVPVSSYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2079629
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 27 27 0 0 0 0 0 0 0 0999 V2000 4.4489 0.7986 -0.7551 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6684 0.8819 0.4210 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3552 0.4136 0.4406 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6205 0.5091 1.6028 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3088 0.0547 1.6653 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2921 -0.5076 0.5537 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6825 -1.0081 0.5594 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6792 0.0560 0.1706 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3555 0.5433 -1.2251 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0005 -0.4982 0.1858 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4669 -0.5899 -0.5945 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7729 -0.1411 -0.6682 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3250 1.4869 -0.6476 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8225 -0.2557 -0.8597 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8694 1.0880 -1.6405 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1132 0.9551 2.4660 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2459 0.1379 2.5788 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7614 -1.8153 -0.1984 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9650 -1.4696 1.5324 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6668 0.9319 0.8410 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3960 1.1069 -1.1951 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2060 -0.3029 -1.9232 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1463 1.2447 -1.5832 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7126 0.1940 0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0246 -1.3080 0.8597 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0465 -1.0209 -1.4934 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3163 -0.2348 -1.6022 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 6 11 1 0 11 12 2 0 12 3 1 0 1 13 1 0 1 14 1 0 1 15 1 0 4 16 1 0 5 17 1 0 7 18 1 0 7 19 1 0 8 20 1 1 9 21 1 0 9 22 1 0 9 23 1 0 10 24 1 0 10 25 1 0 11 26 1 0 12 27 1 0 M END

Standard InCHIKey	NEGYEDYHPHMHGK-MRVPVSSYSA-N
Standard InCHI	InChI=1S/C10H15NO/c1-8(11)7-9-3-5-10(12-2)6-4-9/h3-6,8H,7,11H2,1-2H3/t8-/m1/s1
SMILES	COc1ccc(C[C@@H](C)N)cc1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	165.12	Volume:	184.837 ? Van der Waals volume.
Dense:	0.893	LogP:	2.044 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.849 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.702 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	3.0	Rigid Bonds:	6.0
TPSA:	35.25 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	2.0	Rings:	1.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.738	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.927	Fsp³:	0.4
MCE-18:	12.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.363	Fluc inhibitor:	0.089 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.017 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.523	Promiscuous compounds:	0.111

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.658	MDCK Permeability:	-4.634
Pgp-inhibitor:	0.011	Pgp-substrate:	0.868
PAMPA:	0.093 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.004	30% Bioavailability (F30%):	0.003
50% Bioavailability (F50%):	0.072

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.347	MRP1:	0.313
Plasma Protein Binding (PPB):	32.959%	Volume Distribution (VD):	0.503
Fu:	64.548% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.588
OATP1B3 inhibitor:	0.227	BCRP inhibitor:	0.027
BSEP inhibitor:	0.867

ADMET: Metabolism

CYP1A2-inhibitor:	0.99	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.135	CYP2C9-substrate:	0.989
CYP2D6-inhibitor:	1.0	CYP2D6-substrate:	0.003
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.059	CYP2C8-inhibitor:	0.0
HLM stability:	0.012 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

10.609

Half-life (T1/2):

1.453

ADMET: Toxicity

hERG Blockers:	0.364	hERG Blockers (10um):	0.306
Human Hepatotoxicity (H-HT):	0.863	Drug-induced Liver Injury (DILI):	0.081
AMES Toxicity:	0.262	Rat Oral Acute Toxicity:	0.815
Maximum Recommended Daily Dose:	0.581	Skin Sensitization:	0.933
Carcinogencity:	0.189	Eye Corrosion:	0.965
Eye Irritation:	0.977	Respiratory Toxicity:	0.977
Drug-induced Neurotoxicity:	0.976	Ototoxicity:	0.458
Hematotoxicity:	0.245	Drug-induced Nephrotoxicity:	0.528
Genotoxicity:	0.087	RPMI-8226 Immunitoxicity:	0.048
A549 Cytotoxicity:	0.004	Hek293 Cytotoxicity:	0.068
BCF:	0.428 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.93 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.886 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.23 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO53586	Acacia rigidula Benth.	Genus	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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	Organism Name	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
Kd	3
K	7
No. of animals	3
Activity	1
Total release	1
Relative rate	1
DOM	3
ED50	1

Activity Type	# Activity
Protein family	3
Organism	17

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29423	Protein family	Serotonin (5-HT) receptor	Rattus norvegicus	Kd	=	4168.69	nM	PMID[7365744]
NPT29423	Protein family	Serotonin (5-HT) receptor	Rattus norvegicus	Kd	=	6918.31	nM	PMID[7365744]
NPT29423	Protein family	Serotonin (5-HT) receptor	Rattus norvegicus	Kd	=	4168.69	nM	PMID[7143352]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	2550000.0	min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	No. of animals	=	1.0	n.a.	PMID[7143352]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	2280000.0	min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	No. of animals	=	3.0	n.a.	PMID[7143352]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	<	20.0	%	PMID[28244748]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	1390000.0	min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Total release	=	57.78	%	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	1340000.0	min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	No. of animals	=	5.0	n.a.	PMID[7143352]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Relative rate	=	1.76	n.a.	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	DOM	n.a.	n.a.	n.a.	PMID[7143352]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	3070000.0	min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	2300000.0	min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	K	=	280.0	10e4min-1	PMID[7086839]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	DOM	=	18.0	%	PMID[7143352]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	ED50	=	0.4	mg.kg-1	PMID[28244748]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	DOM	=	20.0	%	PMID[7143352]

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC605225 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24112
0.1-0.2	21302
0.2-0.3	4096
0.3-0.4	294
0.4-0.5	38
0.5-0.6	6
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC97811
0.7586	Intermediate Similarity	NPC26524
0.6364	Remote Similarity	NPC21890
0.6333	Remote Similarity	NPC42383
0.6	Remote Similarity	NPC321956
0.6	Remote Similarity	NPC38209
0.5667	Remote Similarity	NPC71853
0.5625	Remote Similarity	NPC291847
0.5455	Remote Similarity	NPC298224
0.5172	Remote Similarity	NPC112609
0.5172	Remote Similarity	NPC612027
0.5152	Remote Similarity	NPC1065

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC605225 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3127
0.1-0.2	5295
0.2-0.3	656
0.3-0.4	61
0.4-0.5	9
0.5-0.6	2
0.6-0.7	0
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
0.5172	Remote Similarity	NPD9593	Phase 4
0.5172	Remote Similarity	NPD9594	Phase 4

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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