Structure

Physi-Chem Properties

Molecular Weight:  229.18
Volume:  262.71
LogP:  4.488
LogD:  3.833
LogS:  -4.938
# Rotatable Bonds:  0
TPSA:  4.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.525
Synthetic Accessibility Score:  6.043
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.722
MDCK Permeability:  2.1347903384594247e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.705

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.872
Plasma Protein Binding (PPB):  52.699241638183594%
Volume Distribution (VD):  1.187
Pgp-substrate:  54.86024475097656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.181
CYP1A2-substrate:  0.814
CYP2C19-inhibitor:  0.712
CYP2C19-substrate:  0.875
CYP2C9-inhibitor:  0.326
CYP2C9-substrate:  0.274
CYP2D6-inhibitor:  0.422
CYP2D6-substrate:  0.213
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.459

ADMET: Excretion

Clearance (CL):  5.299
Half-life (T1/2):  0.223

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.73
Drug-inuced Liver Injury (DILI):  0.039
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.911
Maximum Recommended Daily Dose:  0.757
Skin Sensitization:  0.42
Carcinogencity:  0.922
Eye Corrosion:  0.853
Eye Irritation:  0.224
Respiratory Toxicity:  0.978

Download Data

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

  Natural Product: NPC472827

Natural Product ID:  NPC472827
Common Name*:   OAWMBCXCDRYTHQ-MAZHCROVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OAWMBCXCDRYTHQ-MAZHCROVSA-N
Standard InCHI:  InChI=1S/C16H23N/c1-14(2)10-13(17-4)16-8-5-7-15(3,11-16)9-6-12(14)16/h10,12H,5-9,11H2,1-3H3/t12-,15+,16-/m0/s1
SMILES:  CC1(C=C(C23C1CCC(C2)(CCC3)C)[N+]#[C-])C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3586298
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO28764 Phyllidia ocellata Species Phyllidiidae Eukaryota n.a. n.a. n.a. PMID[26056748]
NPO28764 Phyllidia ocellata Species Phyllidiidae 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
NPT757 Organism Plasmodium falciparum 3D7 Plasmodium falciparum 3D7 IC50 = 300.0 nM PMID[555872]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 360.0 nM PMID[555872]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum GI = 98.3 % PMID[555872]
NPT2 Others Unspecified Ratio IC50 = 45.0 n.a. PMID[555872]

☑ 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 NPC472827 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
0.8308 Intermediate Similarity NPC472831
0.8065 Intermediate Similarity NPC219621
0.7619 Intermediate Similarity NPC317778
0.7419 Intermediate Similarity NPC474457
0.7419 Intermediate Similarity NPC474415
0.7419 Intermediate Similarity NPC475696
0.7419 Intermediate Similarity NPC474528
0.7344 Intermediate Similarity NPC311809
0.7313 Intermediate Similarity NPC37792
0.7286 Intermediate Similarity NPC265789
0.7241 Intermediate Similarity NPC22765
0.7188 Intermediate Similarity NPC475716
0.7188 Intermediate Similarity NPC474455
0.7188 Intermediate Similarity NPC474420
0.7188 Intermediate Similarity NPC474454
0.7121 Intermediate Similarity NPC474086
0.7042 Intermediate Similarity NPC21773
0.7 Intermediate Similarity NPC184919
0.7 Intermediate Similarity NPC138409
0.6984 Remote Similarity NPC318036
0.6949 Remote Similarity NPC17518
0.6923 Remote Similarity NPC152211
0.6923 Remote Similarity NPC28755
0.6875 Remote Similarity NPC470370
0.6875 Remote Similarity NPC470369
0.6875 Remote Similarity NPC173815
0.6866 Remote Similarity NPC145715
0.6849 Remote Similarity NPC476904
0.6833 Remote Similarity NPC476681
0.678 Remote Similarity NPC124851
0.6774 Remote Similarity NPC474416
0.6769 Remote Similarity NPC472830
0.6769 Remote Similarity NPC324944
0.6765 Remote Similarity NPC473959
0.6724 Remote Similarity NPC86683
0.6667 Remote Similarity NPC192529
0.6667 Remote Similarity NPC7214
0.6623 Remote Similarity NPC211322
0.6571 Remote Similarity NPC474456
0.6562 Remote Similarity NPC469770
0.6533 Remote Similarity NPC125828
0.6508 Remote Similarity NPC472828
0.6508 Remote Similarity NPC476679
0.6491 Remote Similarity NPC193180
0.6447 Remote Similarity NPC476308
0.6351 Remote Similarity NPC476329
0.6329 Remote Similarity NPC12035
0.6316 Remote Similarity NPC103290
0.6308 Remote Similarity NPC123194
0.629 Remote Similarity NPC200129
0.6286 Remote Similarity NPC476682
0.6271 Remote Similarity NPC202189
0.6269 Remote Similarity NPC469769
0.625 Remote Similarity NPC152039
0.625 Remote Similarity NPC118329
0.625 Remote Similarity NPC329782
0.6207 Remote Similarity NPC105246
0.6207 Remote Similarity NPC190232
0.6173 Remote Similarity NPC471868
0.6173 Remote Similarity NPC472312
0.6173 Remote Similarity NPC283277
0.6173 Remote Similarity NPC215474
0.6167 Remote Similarity NPC114239
0.6167 Remote Similarity NPC296337
0.6167 Remote Similarity NPC241784
0.6167 Remote Similarity NPC13991
0.6154 Remote Similarity NPC476683
0.6098 Remote Similarity NPC171639
0.6071 Remote Similarity NPC157479
0.6071 Remote Similarity NPC166458
0.6049 Remote Similarity NPC474122
0.6029 Remote Similarity NPC60772
0.6 Remote Similarity NPC248411
0.6 Remote Similarity NPC127944
0.5952 Remote Similarity NPC311769
0.5952 Remote Similarity NPC24733
0.5952 Remote Similarity NPC182106
0.5952 Remote Similarity NPC75810
0.5915 Remote Similarity NPC472544
0.5904 Remote Similarity NPC21667
0.5902 Remote Similarity NPC49088
0.589 Remote Similarity NPC323005
0.589 Remote Similarity NPC92327
0.5873 Remote Similarity NPC106990
0.5846 Remote Similarity NPC473728
0.5846 Remote Similarity NPC212905
0.5833 Remote Similarity NPC469662
0.5821 Remote Similarity NPC470893
0.5811 Remote Similarity NPC176107
0.5811 Remote Similarity NPC476135
0.5806 Remote Similarity NPC323445
0.5797 Remote Similarity NPC231129
0.5795 Remote Similarity NPC84171
0.5775 Remote Similarity NPC469728
0.5765 Remote Similarity NPC147513
0.5765 Remote Similarity NPC152684
0.5761 Remote Similarity NPC184033
0.5761 Remote Similarity NPC167419
0.5758 Remote Similarity NPC475272
0.5747 Remote Similarity NPC259252
0.5733 Remote Similarity NPC20610
0.5733 Remote Similarity NPC160209
0.5714 Remote Similarity NPC21781
0.5714 Remote Similarity NPC178644
0.5714 Remote Similarity NPC82919
0.5694 Remote Similarity NPC197238
0.5694 Remote Similarity NPC202118
0.5682 Remote Similarity NPC249312
0.5676 Remote Similarity NPC222366
0.5676 Remote Similarity NPC176171
0.5676 Remote Similarity NPC286669
0.5676 Remote Similarity NPC476039
0.5667 Remote Similarity NPC93027
0.5658 Remote Similarity NPC182815
0.5658 Remote Similarity NPC139397
0.5652 Remote Similarity NPC11130
0.5641 Remote Similarity NPC474743
0.5634 Remote Similarity NPC176621
0.5625 Remote Similarity NPC17810
0.5625 Remote Similarity NPC174803
0.5625 Remote Similarity NPC259989
0.5616 Remote Similarity NPC52449
0.5616 Remote Similarity NPC169275
0.5604 Remote Similarity NPC473314
0.56 Remote Similarity NPC220210
0.56 Remote Similarity NPC20181
0.56 Remote Similarity NPC197805

  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 NPC472827 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
0.6438 Remote Similarity NPD6939 Phase 2
0.6438 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6207 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5733 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5365 Phase 2
0.5658 Remote Similarity NPD4137 Phase 3
0.5625 Remote Similarity NPD8262 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