Structure

Physi-Chem Properties

Molecular Weight:  88.09
Volume:  103.827
LogP:  1.041
LogD:  0.809
LogS:  -0.387
# Rotatable Bonds:  2
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.537
Synthetic Accessibility Score:  2.361
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.192
MDCK Permeability:  8.231413085013628e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.909
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.883
Plasma Protein Binding (PPB):  21.206912994384766%
Volume Distribution (VD):  1.102
Pgp-substrate:  66.43238067626953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.272
CYP1A2-substrate:  0.741
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.776
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.385
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.398
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  11.28
Half-life (T1/2):  0.771

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.049
Drug-inuced Liver Injury (DILI):  0.028
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.03
Skin Sensitization:  0.162
Carcinogencity:  0.27
Eye Corrosion:  0.946
Eye Irritation:  0.994
Respiratory Toxicity:  0.093

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC39977

Natural Product ID:  NPC39977
Common Name*:   3-Pentanol
IUPAC Name:   pentan-3-ol
Synonyms:   3-Pentanol; Pentan-3-ol
Standard InCHIKey:  AQIXEPGDORPWBJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H12O/c1-3-5(6)4-2/h5-6H,3-4H2,1-2H3
SMILES:  CCC(CC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL47100
PubChem CID:   11428
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols

*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
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39730000707]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11473412]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. root n.a. PMID[15730255]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[15730255]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[16724861]
NPO26211 Knightia excelsa Species Proteaceae Eukaryota n.a. n.a. n.a. PMID[17315967]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18491868]
NPO26507 Galenia africana Species Aizoaceae Eukaryota leaf n.a. n.a. PMID[20035557]
NPO26654 Penicillium citreonigrum Species Aspergillaceae Eukaryota n.a. atlantic-forest-soil n.a. PMID[20450206]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[21302965]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26566007]
NPO26451 Ophiocoma scolopendrina Species Ophiocomidae Eukaryota n.a. n.a. n.a. PMID[27684202]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[7288445]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26699 Leonurus glaucescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26349 Frullania tamarisci Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25972 Eupolyphaga sinensis Species Corydiidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26699 Leonurus glaucescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26561 Micromeria pineolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26406 Saussurea carthamoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26349 Frullania tamarisci Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25792 Delphinium andersoni Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26900 Vallota purpurea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26374 Alangium premnifolium Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26624 Ilex amara Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26654 Penicillium citreonigrum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25995 Laurencia distichophylla Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26184 Diphasia angolensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26507 Galenia africana Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25972 Eupolyphaga sinensis Species Corydiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26023 Angelica tarokoensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26584 Gnidia lamprantha Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26950 Maba buxifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26319 Solanum acaule Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25896 Bragantia wallichii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26161 Globba malaccensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26806 Nidula candida Species Nidulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7447 Nemalion vermiculare Species Liagoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26451 Ophiocoma scolopendrina Species Ophiocomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2898 Quercus sessiliflora Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25949 Streptomyces griseovariabilis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25923 Vismia jefensis Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26607 Colobocentrotus atratus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26052 Swertia delavayi Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26211 Knightia excelsa Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25739 Erysimum odoratum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26287 Spodoptera eridania Species 0ctuidae 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT27 Others Unspecified EC50 = 7655966069112.57 nM PMID[489854]
NPT27 Others Unspecified LC50 = 11220184543019.65 nM PMID[489854]
NPT27 Others Unspecified log Ks = 1.35 n.a. PMID[489855]
NPT561 Organism Tetrahymena pyriformis Tetrahymena pyriformis GI50 = 57055826.39 nM PMID[489856]

☑ 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 NPC39977 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9545 High Similarity NPC245688
0.9524 High Similarity NPC299484
0.913 High Similarity NPC232554
0.875 High Similarity NPC560
0.8571 High Similarity NPC163707
0.8333 Intermediate Similarity NPC140389
0.8333 Intermediate Similarity NPC88887
0.8333 Intermediate Similarity NPC190797
0.8261 Intermediate Similarity NPC52403
0.8182 Intermediate Similarity NPC294703
0.8095 Intermediate Similarity NPC311000
0.8077 Intermediate Similarity NPC159845
0.8077 Intermediate Similarity NPC52362
0.8 Intermediate Similarity NPC252154
0.7917 Intermediate Similarity NPC114270
0.7826 Intermediate Similarity NPC110344
0.7826 Intermediate Similarity NPC88839
0.7778 Intermediate Similarity NPC110884
0.76 Intermediate Similarity NPC275462
0.7407 Intermediate Similarity NPC325345
0.7241 Intermediate Similarity NPC122962
0.72 Intermediate Similarity NPC87529
0.72 Intermediate Similarity NPC23071
0.72 Intermediate Similarity NPC256186
0.72 Intermediate Similarity NPC199270
0.72 Intermediate Similarity NPC157340
0.72 Intermediate Similarity NPC94144
0.7143 Intermediate Similarity NPC270334
0.7083 Intermediate Similarity NPC219266
0.7037 Intermediate Similarity NPC320326
0.7037 Intermediate Similarity NPC276332
0.7037 Intermediate Similarity NPC39869
0.7037 Intermediate Similarity NPC272307
0.7 Intermediate Similarity NPC66124
0.7 Intermediate Similarity NPC72324
0.7 Intermediate Similarity NPC193062
0.7 Intermediate Similarity NPC1748
0.7 Intermediate Similarity NPC319034
0.6957 Remote Similarity NPC236761
0.6923 Remote Similarity NPC213764
0.6786 Remote Similarity NPC33415
0.6786 Remote Similarity NPC301586
0.6786 Remote Similarity NPC279895
0.6667 Remote Similarity NPC106054
0.6667 Remote Similarity NPC149070
0.6667 Remote Similarity NPC2724
0.6667 Remote Similarity NPC187058
0.6667 Remote Similarity NPC197207
0.6667 Remote Similarity NPC182541
0.6667 Remote Similarity NPC267243
0.6667 Remote Similarity NPC127074
0.6562 Remote Similarity NPC97967
0.6522 Remote Similarity NPC152773
0.6364 Remote Similarity NPC79544
0.6364 Remote Similarity NPC474914
0.6364 Remote Similarity NPC474392
0.6333 Remote Similarity NPC185041
0.6333 Remote Similarity NPC24506
0.6333 Remote Similarity NPC236797
0.6333 Remote Similarity NPC163556
0.6333 Remote Similarity NPC147096
0.6333 Remote Similarity NPC225783
0.6333 Remote Similarity NPC112242
0.6296 Remote Similarity NPC272690
0.6296 Remote Similarity NPC304786
0.625 Remote Similarity NPC81989
0.625 Remote Similarity NPC227267
0.6207 Remote Similarity NPC223195
0.6207 Remote Similarity NPC261397
0.6129 Remote Similarity NPC126915
0.6129 Remote Similarity NPC317060
0.6071 Remote Similarity NPC128335
0.6061 Remote Similarity NPC293908
0.6061 Remote Similarity NPC192065
0.6061 Remote Similarity NPC191084
0.6061 Remote Similarity NPC168052
0.6061 Remote Similarity NPC250870
0.6061 Remote Similarity NPC325034
0.6061 Remote Similarity NPC86412
0.6061 Remote Similarity NPC66052
0.5938 Remote Similarity NPC291158
0.5938 Remote Similarity NPC139131
0.5938 Remote Similarity NPC205141
0.5938 Remote Similarity NPC272998
0.5938 Remote Similarity NPC185538
0.5938 Remote Similarity NPC181516
0.5926 Remote Similarity NPC318912
0.5926 Remote Similarity NPC237965
0.5882 Remote Similarity NPC313405
0.5882 Remote Similarity NPC5505
0.5862 Remote Similarity NPC324353
0.5833 Remote Similarity NPC328688
0.5833 Remote Similarity NPC34153
0.5806 Remote Similarity NPC28077
0.5806 Remote Similarity NPC141902
0.5758 Remote Similarity NPC283682
0.5714 Remote Similarity NPC82694
0.5714 Remote Similarity NPC174396
0.5714 Remote Similarity NPC35155
0.5676 Remote Similarity NPC320331
0.5667 Remote Similarity NPC238135
0.5625 Remote Similarity NPC31433
0.5625 Remote Similarity NPC76217
0.5625 Remote Similarity NPC321170
0.5625 Remote Similarity NPC266566
0.5625 Remote Similarity NPC307739
0.56 Remote Similarity NPC147212

  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 NPC39977 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.8571 High Similarity NPD8224 Approved
0.8095 Intermediate Similarity NPD8223 Approved
0.7917 Intermediate Similarity NPD8225 Phase 3
0.7407 Intermediate Similarity NPD8988 Clinical (unspecified phase)
0.72 Intermediate Similarity NPD8226 Approved
0.6786 Remote Similarity NPD8549 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8814 Phase 3
0.64 Remote Similarity NPD8196 Approved
0.6061 Remote Similarity NPD9053 Approved
0.6061 Remote Similarity NPD9051 Approved
0.6061 Remote Similarity NPD9052 Approved
0.5938 Remote Similarity NPD2272 Approved
0.5938 Remote Similarity NPD5383 Approved
0.5714 Remote Similarity NPD8956 Approved
0.5714 Remote Similarity NPD8231 Approved
0.5714 Remote Similarity NPD8207 Approved
0.5652 Remote Similarity NPD8547 Phase 2
0.5625 Remote Similarity NPD8237 Approved
0.5625 Remote Similarity NPD8202 Approved
0.5625 Remote Similarity NPD8205 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