Structure

Physi-Chem Properties

Molecular Weight:  509.34
Volume:  537.714
LogP:  3.541
LogD:  0.974
LogS:  -2.747
# Rotatable Bonds:  4
TPSA:  102.37
# H-Bond Aceptor:  8
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.454
Synthetic Accessibility Score:  5.404
Fsp3:  0.821
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.891
MDCK Permeability:  5.399821748142131e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.067
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.106

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.072
Plasma Protein Binding (PPB):  77.30853271484375%
Volume Distribution (VD):  2.422
Pgp-substrate:  11.099371910095215%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.11
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.95
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.186
CYP3A4-inhibitor:  0.75
CYP3A4-substrate:  0.781

ADMET: Excretion

Clearance (CL):  8.594
Half-life (T1/2):  0.207

ADMET: Toxicity

hERG Blockers:  0.104
Human Hepatotoxicity (H-HT):  0.683
Drug-inuced Liver Injury (DILI):  0.909
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.145
Maximum Recommended Daily Dose:  0.097
Skin Sensitization:  0.341
Carcinogencity:  0.346
Eye Corrosion:  0.016
Eye Irritation:  0.013
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC60424

Natural Product ID:  NPC60424
Common Name*:   2,5-Dihydrophenylalanine
IUPAC Name:   (2S)-2-amino-3-cyclohexa-1,4-dien-1-ylpropanoic acid
Synonyms:  
Standard InCHIKey:  FSZMHEMPLAVBQZ-QMMMGPOBSA-N
Standard InCHI:  InChI=1S/C9H13NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-2,5,8H,3-4,6,10H2,(H,11,12)/t8-/m0/s1
SMILES:  C1=CCC(=CC1)C[C@@H](C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3251934
PubChem CID:   441444
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

*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
NPO15932 Coriaria sinica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15932 Coriaria sinica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22597 Parmelia kamtschadalis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11133 Euphorbia x bothae Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22223 Jurinea cyanoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22412 Siphocampylus westinianus Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15932 Coriaria sinica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22947 Streptomyces coerulescens Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20227 Baccharis boliviensis Species Asteraceae 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
NPT2 Others Unspecified Ki = 230000.0 nM PMID[532792]

☑ 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 NPC60424 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 NPC314221
0.75 Intermediate Similarity NPC133700
0.7097 Intermediate Similarity NPC324825
0.7097 Intermediate Similarity NPC112890
0.7097 Intermediate Similarity NPC316231
0.6962 Remote Similarity NPC157173
0.6901 Remote Similarity NPC50047
0.6667 Remote Similarity NPC207292
0.6667 Remote Similarity NPC183845
0.6667 Remote Similarity NPC279661
0.662 Remote Similarity NPC47333
0.6618 Remote Similarity NPC278209
0.6593 Remote Similarity NPC122493
0.6593 Remote Similarity NPC10781
0.6593 Remote Similarity NPC293628
0.6593 Remote Similarity NPC324569
0.6562 Remote Similarity NPC5413
0.6562 Remote Similarity NPC149821
0.6557 Remote Similarity NPC323974
0.6556 Remote Similarity NPC40663
0.6522 Remote Similarity NPC176164
0.6522 Remote Similarity NPC189301
0.6452 Remote Similarity NPC118459
0.6452 Remote Similarity NPC327698
0.6429 Remote Similarity NPC276928
0.6429 Remote Similarity NPC254541
0.6429 Remote Similarity NPC268927
0.6429 Remote Similarity NPC320598
0.6429 Remote Similarity NPC64250
0.6406 Remote Similarity NPC93081
0.6406 Remote Similarity NPC140872
0.6395 Remote Similarity NPC202056
0.6364 Remote Similarity NPC28205
0.6308 Remote Similarity NPC43204
0.6308 Remote Similarity NPC84636
0.6308 Remote Similarity NPC245027
0.6308 Remote Similarity NPC62045
0.6308 Remote Similarity NPC226027
0.6308 Remote Similarity NPC162620
0.6308 Remote Similarity NPC174246
0.6279 Remote Similarity NPC90476
0.6279 Remote Similarity NPC69374
0.6269 Remote Similarity NPC281245
0.6269 Remote Similarity NPC92114
0.6267 Remote Similarity NPC113224
0.6212 Remote Similarity NPC50457
0.6207 Remote Similarity NPC258824
0.6197 Remote Similarity NPC325734
0.6176 Remote Similarity NPC321062
0.6176 Remote Similarity NPC70387
0.6176 Remote Similarity NPC139029
0.6176 Remote Similarity NPC1813
0.6176 Remote Similarity NPC294548
0.6176 Remote Similarity NPC36061
0.6154 Remote Similarity NPC91495
0.6154 Remote Similarity NPC315199
0.6122 Remote Similarity NPC67043
0.6119 Remote Similarity NPC155512
0.6119 Remote Similarity NPC284212
0.6119 Remote Similarity NPC48162
0.6111 Remote Similarity NPC236322
0.6111 Remote Similarity NPC319021
0.6111 Remote Similarity NPC68974
0.6094 Remote Similarity NPC117572
0.6087 Remote Similarity NPC87564
0.6087 Remote Similarity NPC6095
0.6087 Remote Similarity NPC154245
0.6087 Remote Similarity NPC32467
0.6087 Remote Similarity NPC85813
0.6087 Remote Similarity NPC290563
0.6087 Remote Similarity NPC424
0.6087 Remote Similarity NPC25417
0.6087 Remote Similarity NPC88966
0.6087 Remote Similarity NPC281972
0.6087 Remote Similarity NPC261831
0.6082 Remote Similarity NPC164859
0.6081 Remote Similarity NPC316674
0.6056 Remote Similarity NPC319279
0.6056 Remote Similarity NPC168308
0.6056 Remote Similarity NPC302569
0.6 Remote Similarity NPC274290
0.6 Remote Similarity NPC473863
0.6 Remote Similarity NPC54766
0.6 Remote Similarity NPC304455
0.5974 Remote Similarity NPC98329
0.5974 Remote Similarity NPC7392
0.597 Remote Similarity NPC273330
0.597 Remote Similarity NPC137958
0.597 Remote Similarity NPC59051
0.5941 Remote Similarity NPC298484
0.5918 Remote Similarity NPC469895
0.5915 Remote Similarity NPC18951
0.5915 Remote Similarity NPC477201
0.5915 Remote Similarity NPC179764
0.5915 Remote Similarity NPC187777
0.5909 Remote Similarity NPC180534
0.59 Remote Similarity NPC327481
0.5882 Remote Similarity NPC178586
0.5875 Remote Similarity NPC320669
0.5875 Remote Similarity NPC318814
0.5873 Remote Similarity NPC276294
0.5844 Remote Similarity NPC322035
0.5844 Remote Similarity NPC188231
0.5844 Remote Similarity NPC222327
0.5844 Remote Similarity NPC166791
0.5844 Remote Similarity NPC100719
0.5833 Remote Similarity NPC225929
0.5825 Remote Similarity NPC319579
0.5806 Remote Similarity NPC326992
0.5806 Remote Similarity NPC168375
0.5806 Remote Similarity NPC121517
0.5797 Remote Similarity NPC129458
0.5797 Remote Similarity NPC190184
0.5797 Remote Similarity NPC216407
0.5797 Remote Similarity NPC197087
0.5789 Remote Similarity NPC278881
0.5789 Remote Similarity NPC234767
0.5781 Remote Similarity NPC132307
0.5781 Remote Similarity NPC126925
0.5781 Remote Similarity NPC325097
0.5773 Remote Similarity NPC12730
0.5769 Remote Similarity NPC107224
0.5769 Remote Similarity NPC329011
0.5765 Remote Similarity NPC314762
0.5758 Remote Similarity NPC42304
0.5753 Remote Similarity NPC327748
0.5753 Remote Similarity NPC316826
0.5753 Remote Similarity NPC321468
0.5753 Remote Similarity NPC267817
0.5753 Remote Similarity NPC34416
0.5753 Remote Similarity NPC317143
0.5735 Remote Similarity NPC224227
0.5733 Remote Similarity NPC125312
0.5733 Remote Similarity NPC174560
0.5733 Remote Similarity NPC273614
0.5714 Remote Similarity NPC10081
0.5714 Remote Similarity NPC145235
0.5714 Remote Similarity NPC474584
0.5714 Remote Similarity NPC225066
0.5696 Remote Similarity NPC15864
0.5694 Remote Similarity NPC318260
0.5694 Remote Similarity NPC317147
0.5694 Remote Similarity NPC325977
0.5692 Remote Similarity NPC329263
0.5679 Remote Similarity NPC315897
0.5676 Remote Similarity NPC274927
0.5676 Remote Similarity NPC327170
0.5676 Remote Similarity NPC329550
0.5676 Remote Similarity NPC106851
0.5676 Remote Similarity NPC329564
0.567 Remote Similarity NPC132931
0.5663 Remote Similarity NPC212008
0.5663 Remote Similarity NPC51055
0.5663 Remote Similarity NPC3094
0.5663 Remote Similarity NPC62293
0.5663 Remote Similarity NPC140327
0.5658 Remote Similarity NPC55068
0.5658 Remote Similarity NPC477707
0.5657 Remote Similarity NPC72401
0.5657 Remote Similarity NPC325339
0.5652 Remote Similarity NPC262968
0.5634 Remote Similarity NPC322461
0.5634 Remote Similarity NPC2801
0.5634 Remote Similarity NPC87394
0.5634 Remote Similarity NPC137538
0.5625 Remote Similarity NPC291186
0.5625 Remote Similarity NPC471257
0.5625 Remote Similarity NPC167986
0.5625 Remote Similarity NPC3604
0.5616 Remote Similarity NPC190385
0.5616 Remote Similarity NPC11433
0.5616 Remote Similarity NPC245346
0.5616 Remote Similarity NPC302003
0.5612 Remote Similarity NPC239768
0.5612 Remote Similarity NPC128698
0.561 Remote Similarity NPC26932
0.5604 Remote Similarity NPC472614
0.56 Remote Similarity NPC251042
0.56 Remote Similarity NPC243532
0.56 Remote Similarity NPC302188
0.56 Remote Similarity NPC235242
0.56 Remote Similarity NPC174447
0.56 Remote Similarity NPC122521

  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 NPC60424 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
0.7344 Intermediate Similarity NPD8971 Approved
0.7286 Intermediate Similarity NPD9201 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD9016 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD9044 Approved
0.6835 Remote Similarity NPD3732 Approved
0.6593 Remote Similarity NPD9566 Approved
0.6562 Remote Similarity NPD3173 Approved
0.6557 Remote Similarity NPD9019 Approved
0.6406 Remote Similarity NPD8809 Approved
0.6406 Remote Similarity NPD8808 Approved
0.6386 Remote Similarity NPD857 Phase 3
0.6308 Remote Similarity NPD9017 Approved
0.6308 Remote Similarity NPD9018 Approved
0.6203 Remote Similarity NPD9109 Discontinued
0.6176 Remote Similarity NPD3172 Approved
0.6094 Remote Similarity NPD4222 Approved
0.6094 Remote Similarity NPD3174 Discontinued
0.6087 Remote Similarity NPD3194 Approved
0.6087 Remote Similarity NPD3196 Approved
0.6087 Remote Similarity NPD3195 Phase 2
0.6087 Remote Similarity NPD4266 Approved
0.6056 Remote Similarity NPD9439 Approved
0.6056 Remote Similarity NPD9438 Approved
0.6053 Remote Similarity NPD9421 Phase 1
0.6 Remote Similarity NPD9454 Approved
0.5974 Remote Similarity NPD9137 Approved
0.597 Remote Similarity NPD8872 Phase 3
0.597 Remote Similarity NPD8871 Approved
0.5946 Remote Similarity NPD9676 Phase 3
0.5918 Remote Similarity NPD2258 Approved
0.5918 Remote Similarity NPD2259 Approved
0.5909 Remote Similarity NPD622 Approved
0.587 Remote Similarity NPD1749 Approved
0.5846 Remote Similarity NPD39 Approved
0.5833 Remote Similarity NPD253 Approved
0.5797 Remote Similarity NPD8785 Approved
0.5797 Remote Similarity NPD8851 Phase 1
0.5781 Remote Similarity NPD8798 Approved
0.5775 Remote Similarity NPD8981 Clinical (unspecified phase)
0.5775 Remote Similarity NPD8980 Approved
0.5775 Remote Similarity NPD8979 Approved
0.5769 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5732 Remote Similarity NPD632 Discontinued
0.5679 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5658 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5652 Remote Similarity NPD29 Approved
0.5652 Remote Similarity NPD28 Approved
0.5625 Remote Similarity NPD8805 Approved
0.5625 Remote Similarity NPD8804 Approved
0.5616 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5616 Remote Similarity NPD8865 Approved
0.5616 Remote Similarity NPD9433 Approved
0.561 Remote Similarity NPD9217 Clinical (unspecified phase)
0.5607 Remote Similarity NPD747 Discontinued
0.56 Remote Similarity NPD9656 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