Structure

Physi-Chem Properties

Molecular Weight:  145.15
Volume:  166.711
LogP:  0.612
LogD:  -0.047
LogS:  0.494
# Rotatable Bonds:  4
TPSA:  46.25
# H-Bond Aceptor:  2
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.626
Synthetic Accessibility Score:  2.892
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:  -4.818
MDCK Permeability:  8.655489364173263e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.042
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.603
Plasma Protein Binding (PPB):  28.717815399169922%
Volume Distribution (VD):  0.89
Pgp-substrate:  80.95298767089844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.028
CYP1A2-substrate:  0.109
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.598
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.195
CYP2D6-inhibitor:  0.056
CYP2D6-substrate:  0.857
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.24

ADMET: Excretion

Clearance (CL):  9.293
Half-life (T1/2):  0.464

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.087
Drug-inuced Liver Injury (DILI):  0.035
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.748
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.302
Carcinogencity:  0.343
Eye Corrosion:  0.726
Eye Irritation:  0.195
Respiratory Toxicity:  0.839

Download Data

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

  Natural Product: NPC193872

Natural Product ID:  NPC193872
Common Name*:   Heptaminol
IUPAC Name:   6-amino-2-methylheptan-2-ol
Synonyms:   Heptaminol
Standard InCHIKey:  LREQLEBVOXIEOM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H19NO/c1-7(9)5-4-6-8(2,3)10/h7,10H,4-6,9H2,1-3H3
SMILES:  CC(CCCC(C)(C)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2111076
PubChem CID:   3590
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary 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
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[12088434]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21707257]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12935 Thymus quinquecostatus Species Lamiaceae 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
NPT1305 Individual Protein Voltage-dependent L-type calcium channel subunit alpha-1C Cavia porcellus IC50 = 15300.0 nM PMID[573198]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Hit score = 0.1609 n.a. PMID[573199]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[573200]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[573200]

☑ 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 NPC193872 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
0.7255 Intermediate Similarity NPC29222
0.7255 Intermediate Similarity NPC96966
0.7255 Intermediate Similarity NPC121062
0.6727 Remote Similarity NPC474322
0.6727 Remote Similarity NPC123814
0.6275 Remote Similarity NPC222078
0.6271 Remote Similarity NPC8979
0.619 Remote Similarity NPC313420
0.6167 Remote Similarity NPC168308
0.6167 Remote Similarity NPC302569
0.6042 Remote Similarity NPC328441
0.5968 Remote Similarity NPC319131
0.5893 Remote Similarity NPC162620
0.5893 Remote Similarity NPC245027
0.5893 Remote Similarity NPC62045
0.5873 Remote Similarity NPC314510
0.5846 Remote Similarity NPC41429
0.5806 Remote Similarity NPC216415
0.5806 Remote Similarity NPC476537
0.5789 Remote Similarity NPC50457
0.5781 Remote Similarity NPC47333
0.5781 Remote Similarity NPC17455
0.5763 Remote Similarity NPC183845
0.5763 Remote Similarity NPC279661
0.5738 Remote Similarity NPC278209
0.5694 Remote Similarity NPC477002
0.5652 Remote Similarity NPC473710
0.5652 Remote Similarity NPC475694
0.5645 Remote Similarity NPC176164
0.5645 Remote Similarity NPC189301
0.5645 Remote Similarity NPC319279
0.5625 Remote Similarity NPC57846
0.5625 Remote Similarity NPC474014
0.5625 Remote Similarity NPC30126
0.5625 Remote Similarity NPC112398
0.5625 Remote Similarity NPC302188
0.5614 Remote Similarity NPC226027
0.5614 Remote Similarity NPC324825
0.5614 Remote Similarity NPC84636
0.5614 Remote Similarity NPC316231
0.5614 Remote Similarity NPC174246
0.5614 Remote Similarity NPC112890
0.5614 Remote Similarity NPC43204
0.5606 Remote Similarity NPC474928
0.56 Remote Similarity NPC277333

  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 NPC193872 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
0.6981 Remote Similarity NPD3214 Discontinued
0.6727 Remote Similarity NPD3215 Phase 1
0.629 Remote Similarity NPD9676 Phase 3
0.6102 Remote Similarity NPD9454 Approved
0.5893 Remote Similarity NPD9018 Approved
0.5893 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5849 Remote Similarity NPD9062 Phase 2
0.5818 Remote Similarity NPD379 Clinical (unspecified phase)
0.5686 Remote Similarity NPD9453 Phase 3
0.566 Remote Similarity NPD718 Approved
0.566 Remote Similarity NPD390 Approved
0.5645 Remote Similarity NPD9439 Approved
0.5645 Remote Similarity NPD9438 Approved
0.5625 Remote Similarity NPD9656 Approved
0.5614 Remote Similarity NPD9044 Approved
0.5614 Remote Similarity NPD9017 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