Structure

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Physi-Chem Properties

Molecular Weight:  204.09
Volume:  208.091
LogP:  -1.234
LogD:  0.069
LogS:  -1.764
# Rotatable Bonds:  3
TPSA:  79.11
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.701
Synthetic Accessibility Score:  2.301
Fsp3:  0.182
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.166
MDCK Permeability:  1.799100573407486e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.101
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.765
Plasma Protein Binding (PPB):  33.6124153137207%
Volume Distribution (VD):  0.356
Pgp-substrate:  70.83013153076172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.126
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.068
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.659
CYP2D6-inhibitor:  0.089
CYP2D6-substrate:  0.549
CYP3A4-inhibitor:  0.019
CYP3A4-substrate:  0.058

ADMET: Excretion

Clearance (CL):  11.879
Half-life (T1/2):  0.873

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.085
Drug-inuced Liver Injury (DILI):  0.023
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.871
Maximum Recommended Daily Dose:  0.059
Skin Sensitization:  0.372
Carcinogencity:  0.111
Eye Corrosion:  0.005
Eye Irritation:  0.072
Respiratory Toxicity:  0.243

Download Data

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

  Natural Product: NPC203468

Natural Product ID:  NPC203468
Common Name*:   Tryptophan
IUPAC Name:   (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid
Synonyms:   Gppe Pdr Sach; L-Tryptophan; Optimax; Optimax Wv; Pacitron; Tryptophan
Standard InCHIKey:  QIVBCDIJIAJPQS-VIFPVBQESA-N
Standard InCHI:  InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1
SMILES:  c1ccc2c(c1)c(C[C@@H](C(=O)O)N)c[nH]2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL54976
PubChem CID:   6305
6923516
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0001290] Indolyl carboxylic acids and derivatives

*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

☑ 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

☑ 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

☑ 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 NPC203468 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

  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 NPC203468 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

  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