Structure

Physi-Chem Properties

Molecular Weight:  75.07
Volume:  80.231
LogP:  -0.679
LogD:  -1.351
LogS:  1.051
# Rotatable Bonds:  1
TPSA:  46.25
# H-Bond Aceptor:  2
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.434
Synthetic Accessibility Score:  2.715
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:  -5.294
MDCK Permeability:  0.0036682835780084133
Pgp-inhibitor:  0.0
Pgp-substrate:  0.165
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.309
Plasma Protein Binding (PPB):  8.080865859985352%
Volume Distribution (VD):  0.822
Pgp-substrate:  90.26764678955078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.042
CYP1A2-substrate:  0.078
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.307
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.065
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.647
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.186

ADMET: Excretion

Clearance (CL):  6.623
Half-life (T1/2):  0.679

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.301
Drug-inuced Liver Injury (DILI):  0.052
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.537
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.411
Carcinogencity:  0.766
Eye Corrosion:  0.89
Eye Irritation:  0.926
Respiratory Toxicity:  0.654

Download Data

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

  Natural Product: NPC84444

Natural Product ID:  NPC84444
Common Name*:   L-Alaninol
IUPAC Name:   (2S)-2-aminopropan-1-ol
Synonyms:  
Standard InCHIKey:  BKMMTJMQCTUHRP-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C3H9NO/c1-3(4)2-5/h3,5H,2,4H2,1H3/t3-/m0/s1
SMILES:  C[C@@H](CO)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1229871
PubChem CID:   80307
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002460] Alkanolamines
            • [CHEMONTID:0001897] 1,2-aminoalcohols

*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
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. PMID[19919095]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota flower buds and leaves Khon Kaen province, Thailand 2010 PMID[23270663]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Leaves n.a. n.a. PMID[23642481]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Flowers n.a. n.a. PMID[26462418]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3478 Nelumbo nucifera Species Nelumbonaceae 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
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 73.39 % PMID[455989]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 104.0 % PMID[455989]

☑ 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 NPC84444 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
1.0 High Similarity NPC145217
0.8387 Intermediate Similarity NPC141902
0.7931 Intermediate Similarity NPC262962
0.7059 Intermediate Similarity NPC313303
0.6757 Remote Similarity NPC21290
0.6757 Remote Similarity NPC116709
0.6757 Remote Similarity NPC272614
0.675 Remote Similarity NPC219143
0.675 Remote Similarity NPC226265
0.6667 Remote Similarity NPC328729
0.6591 Remote Similarity NPC96966
0.6591 Remote Similarity NPC121062
0.6591 Remote Similarity NPC29222
0.65 Remote Similarity NPC168375
0.65 Remote Similarity NPC121517
0.65 Remote Similarity NPC326992
0.65 Remote Similarity NPC53449
0.6444 Remote Similarity NPC270805
0.6444 Remote Similarity NPC93888
0.6341 Remote Similarity NPC105488
0.619 Remote Similarity NPC167986
0.619 Remote Similarity NPC291186
0.6176 Remote Similarity NPC136014
0.6154 Remote Similarity NPC63621
0.6129 Remote Similarity NPC318947
0.6098 Remote Similarity NPC66043
0.6098 Remote Similarity NPC237525
0.6098 Remote Similarity NPC326212
0.6047 Remote Similarity NPC126925
0.6047 Remote Similarity NPC198301
0.6047 Remote Similarity NPC325097
0.6047 Remote Similarity NPC132307
0.6042 Remote Similarity NPC474322
0.6042 Remote Similarity NPC123814
0.6 Remote Similarity NPC136159
0.6 Remote Similarity NPC181588
0.5946 Remote Similarity NPC328698
0.5946 Remote Similarity NPC292422
0.5909 Remote Similarity NPC327698
0.5909 Remote Similarity NPC118459
0.5862 Remote Similarity NPC311000
0.5833 Remote Similarity NPC325909
0.5778 Remote Similarity NPC297220
0.5778 Remote Similarity NPC309658
0.5745 Remote Similarity NPC286989
0.5714 Remote Similarity NPC329495
0.5652 Remote Similarity NPC204364
0.56 Remote Similarity NPC272396

  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 NPC84444 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
0.7059 Intermediate Similarity NPD8558 Approved
0.7059 Intermediate Similarity NPD8557 Approved
0.6757 Remote Similarity NPD8211 Approved
0.6757 Remote Similarity NPD8210 Phase 3
0.675 Remote Similarity NPD8216 Approved
0.675 Remote Similarity NPD8217 Clinical (unspecified phase)
0.6744 Remote Similarity NPD398 Approved
0.6744 Remote Similarity NPD400 Approved
0.6744 Remote Similarity NPD399 Approved
0.6667 Remote Similarity NPD8556 Phase 3
0.6486 Remote Similarity NPD9112 Discontinued
0.6444 Remote Similarity NPD8624 Approved
0.6341 Remote Similarity NPD8197 Approved
0.6341 Remote Similarity NPD8198 Approved
0.6304 Remote Similarity NPD3214 Discontinued
0.619 Remote Similarity NPD8804 Approved
0.619 Remote Similarity NPD8805 Approved
0.6176 Remote Similarity NPD8819 Approved
0.6176 Remote Similarity NPD8817 Phase 3
0.6176 Remote Similarity NPD8818 Approved
0.6176 Remote Similarity NPD8820 Approved
0.6176 Remote Similarity NPD8821 Approved
0.6176 Remote Similarity NPD110 Approved
0.6176 Remote Similarity NPD9262 Approved
0.6047 Remote Similarity NPD8798 Approved
0.6042 Remote Similarity NPD3215 Phase 1
0.6 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5957 Remote Similarity NPD9025 Approved
0.5862 Remote Similarity NPD8223 Approved
0.5641 Remote Similarity NPD8178 Approved
0.5641 Remote Similarity NPD8177 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