NPASS Compound

Natural Product: NPC521637

Natural Product ID	NPC521637
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-Methylbutyl heptanoate
IUPAC Name	isopentyl heptanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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 38 37 0 0 0 0 0 0 0 0999 V2000 5.0256 0.6634 0.3625 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6500 -0.5243 -0.5046 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1308 -1.6230 0.3227 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9730 -1.2944 1.1656 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6794 -0.8809 0.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5331 0.3587 -0.1717 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0687 0.4973 -0.5013 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3167 1.4679 -1.1677 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8127 -0.4446 -0.0634 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2040 -0.4145 -0.3135 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8551 0.8286 0.2492 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3442 0.7231 -0.0947 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0841 1.9293 0.4306 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8956 -0.5501 0.4958 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1974 1.4060 0.2910 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0938 0.3132 1.4108 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9979 1.1053 0.0755 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6730 -0.9030 -0.8958 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0674 -0.2398 -1.3545 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9234 -2.5436 -0.3130 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0010 -1.9933 0.9763 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7619 -2.2155 1.8135 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2595 -0.5399 1.9771 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9675 -0.8145 1.5108 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1979 -1.7138 0.0151 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7998 1.2631 0.4489 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0434 0.3549 -1.1321 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6560 -1.2815 0.2142 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4645 -0.4862 -1.3738 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5011 1.7546 -0.2163 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7084 0.9213 1.3370 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4371 0.7304 -1.1996 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1078 1.9073 0.0171 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0865 1.9495 1.5443 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5627 2.8379 0.0256 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7649 -1.3519 -0.2674 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9566 -0.4091 0.7337 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2865 -0.7877 1.4137 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 1 15 1 0 1 16 1 0 1 17 1 0 2 18 1 0 2 19 1 0 3 20 1 0 3 21 1 0 4 22 1 0 4 23 1 0 5 24 1 0 5 25 1 0 6 26 1 0 6 27 1 0 10 28 1 0 10 29 1 0 11 30 1 0 11 31 1 0 12 32 1 0 13 33 1 0 13 34 1 0 13 35 1 0 14 36 1 0 14 37 1 0 14 38 1 0 M END

Standard InCHIKey	AFCXVDRTNQNGHS-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C12H24O2/c1-4-5-6-7-8-12(13)14-10-9-11(2)3/h11H,4-10H2,1-3H3
SMILES	CCCCCCC(=O)OCCC(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	200.18	Volume:	231.052 ? Van der Waals volume.
Dense:	0.866	LogP:	4.279 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.388 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.817 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	1.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.442	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.788	Fsp³:	0.917
MCE-18:	0.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.027	Fluc inhibitor:	0.021 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.003 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.999	Promiscuous compounds:	0.111

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.017	MDCK Permeability:	-4.631
Pgp-inhibitor:	0.024	Pgp-substrate:	0.149
PAMPA:	0.065 ? 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):	0.007
20% Bioavailability (F20%):	0.053	30% Bioavailability (F30%):	0.059
50% Bioavailability (F50%):	0.395

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.43	MRP1:	0.987
Plasma Protein Binding (PPB):	95.15%	Volume Distribution (VD):	0.289
Fu:	5.069% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.033
OATP1B3 inhibitor:	0.551	BCRP inhibitor:	0.139
BSEP inhibitor:	0.887

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.002	CYP2C19-substrate:	0.997
CYP2C9-inhibitor:	0.102	CYP2C9-substrate:	0.798
CYP2D6-inhibitor:	0.018	CYP2D6-substrate:	0.186
CYP3A4-inhibitor:	0.521	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.041	CYP2C8-inhibitor:	0.996
HLM stability:	0.983 ? 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):

6.997

Half-life (T1/2):

0.382

ADMET: Toxicity

hERG Blockers:	0.172	hERG Blockers (10um):	0.649
Human Hepatotoxicity (H-HT):	0.335	Drug-induced Liver Injury (DILI):	0.14
AMES Toxicity:	0.168	Rat Oral Acute Toxicity:	0.167
Maximum Recommended Daily Dose:	0.165	Skin Sensitization:	0.821
Carcinogencity:	0.539	Eye Corrosion:	0.978
Eye Irritation:	0.994	Respiratory Toxicity:	0.509
Drug-induced Neurotoxicity:	0.136	Ototoxicity:	0.186
Hematotoxicity:	0.179	Drug-induced Nephrotoxicity:	0.277
Genotoxicity:	0.001	RPMI-8226 Immunitoxicity:	0.05
A549 Cytotoxicity:	0.019	Hek293 Cytotoxicity:	0.038
BCF:	1.785 ? 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:	4.049 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.189 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.901 ? 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
NPO62365	Aspergillus clavatus NRRL 1	Species	Aspergillaceae	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

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

In vivo activity

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

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 NPC521637 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	21499
0.1-0.2	25593
0.2-0.3	2453
0.3-0.4	201
0.4-0.5	61
0.5-0.6	31
0.6-0.7	14
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	Natural Product ID
0.76	Intermediate Similarity	NPC178643
0.7407	Intermediate Similarity	NPC603612
0.7143	Intermediate Similarity	NPC149299
0.6923	Remote Similarity	NPC250028
0.6923	Remote Similarity	NPC236579
0.6923	Remote Similarity	NPC80234
0.6923	Remote Similarity	NPC203531
0.6923	Remote Similarity	NPC256163
0.6923	Remote Similarity	NPC40597
0.6786	Remote Similarity	NPC80396
0.6786	Remote Similarity	NPC154642
0.6207	Remote Similarity	NPC80641
0.6154	Remote Similarity	NPC53541
0.6071	Remote Similarity	NPC223249
0.6071	Remote Similarity	NPC476550
0.6061	Remote Similarity	NPC223677
0.6	Remote Similarity	NPC310746
0.5938	Remote Similarity	NPC163345
0.5926	Remote Similarity	NPC168714
0.5862	Remote Similarity	NPC154396
0.5862	Remote Similarity	NPC286695
0.5806	Remote Similarity	NPC26253
0.5714	Remote Similarity	NPC81263
0.5667	Remote Similarity	NPC600941
0.5625	Remote Similarity	NPC488257
0.5625	Remote Similarity	NPC469937
0.5625	Remote Similarity	NPC94699
0.5625	Remote Similarity	NPC128061
0.5625	Remote Similarity	NPC320588
0.5625	Remote Similarity	NPC53463
0.5556	Remote Similarity	NPC201622
0.5556	Remote Similarity	NPC305660
0.5556	Remote Similarity	NPC12156
0.5556	Remote Similarity	NPC161097
0.5556	Remote Similarity	NPC28598
0.5556	Remote Similarity	NPC326758
0.5556	Remote Similarity	NPC22903
0.5556	Remote Similarity	NPC54980
0.5517	Remote Similarity	NPC12904
0.5455	Remote Similarity	NPC55678
0.5385	Remote Similarity	NPC281943
0.5172	Remote Similarity	NPC47363
0.5172	Remote Similarity	NPC287231
0.5172	Remote Similarity	NPC317128
0.5161	Remote Similarity	NPC305182
0.5152	Remote Similarity	NPC308301
0.5143	Remote Similarity	NPC28779
0.5143	Remote Similarity	NPC609455

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC521637 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6035
0.1-0.2	2881
0.2-0.3	202
0.3-0.4	25
0.4-0.5	2
0.5-0.6	5
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
0.5455	Remote Similarity	NPD6125	Phase 4
0.5357	Remote Similarity	NPD900	Pre-clinical
0.5278	Remote Similarity	NPD631	Phase 4
0.5172	Remote Similarity	NPD2699	Pre-clinical
0.5135	Remote Similarity	NPD630	Approved

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