Structure

Physi-Chem Properties

Molecular Weight:  231.2
Volume:  271.267
LogP:  4.96
LogD:  4.773
LogS:  -5.42
# Rotatable Bonds:  1
TPSA:  4.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.455
Synthetic Accessibility Score:  4.703
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:  -4.452
MDCK Permeability:  2.7819436581921764e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.488
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.631

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.392
Plasma Protein Binding (PPB):  95.9585189819336%
Volume Distribution (VD):  2.031
Pgp-substrate:  3.844130516052246%

ADMET: Metabolism

CYP1A2-inhibitor:  0.565
CYP1A2-substrate:  0.282
CYP2C19-inhibitor:  0.136
CYP2C19-substrate:  0.78
CYP2C9-inhibitor:  0.255
CYP2C9-substrate:  0.088
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.138
CYP3A4-inhibitor:  0.18
CYP3A4-substrate:  0.418

ADMET: Excretion

Clearance (CL):  6.032
Half-life (T1/2):  0.316

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.771
Drug-inuced Liver Injury (DILI):  0.41
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.206
Maximum Recommended Daily Dose:  0.505
Skin Sensitization:  0.278
Carcinogencity:  0.095
Eye Corrosion:  0.896
Eye Irritation:  0.95
Respiratory Toxicity:  0.957

Download Data

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

  Natural Product: NPC472830

Natural Product ID:  NPC472830
Common Name*:   HXCRPJICJKTMKQ-KLHDSHLOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HXCRPJICJKTMKQ-KLHDSHLOSA-N
Standard InCHI:  InChI=1S/C16H25N/c1-11(2)13-8-9-16(4)14(13)10-12(3)6-7-15(16)17-5/h10-11,13-15H,6-9H2,1-4H3/t13-,14-,15-,16-/m1/s1
SMILES:  CC1=CC2C(CCC2(C(CC1)[N+]#[C-])C)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3586301
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 870.0 nM PMID[520497]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum GI = 98.3 % PMID[520497]
NPT757 Organism Plasmodium falciparum 3D7 Plasmodium falciparum 3D7 IC50 = 260.0 nM PMID[520497]
NPT2 Others Unspecified Ratio IC50 = 45.0 n.a. PMID[520497]

☑ 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 NPC472830 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
0.7903 Intermediate Similarity NPC219621
0.7571 Intermediate Similarity NPC125828
0.7455 Intermediate Similarity NPC49088
0.7391 Intermediate Similarity NPC21773
0.7321 Intermediate Similarity NPC323445
0.7222 Intermediate Similarity NPC473912
0.7183 Intermediate Similarity NPC476904
0.7164 Intermediate Similarity NPC37792
0.7143 Intermediate Similarity NPC265789
0.6986 Remote Similarity NPC7214
0.6769 Remote Similarity NPC472827
0.6716 Remote Similarity NPC474086
0.6667 Remote Similarity NPC311809
0.6623 Remote Similarity NPC12035
0.661 Remote Similarity NPC178644
0.6538 Remote Similarity NPC152039
0.6538 Remote Similarity NPC118329
0.6538 Remote Similarity NPC474122
0.6538 Remote Similarity NPC329782
0.65 Remote Similarity NPC106990
0.6494 Remote Similarity NPC211322
0.6491 Remote Similarity NPC90506
0.6491 Remote Similarity NPC23145
0.6491 Remote Similarity NPC90803
0.6456 Remote Similarity NPC215474
0.6456 Remote Similarity NPC283277
0.6456 Remote Similarity NPC472312
0.6418 Remote Similarity NPC317778
0.6393 Remote Similarity NPC200129
0.6375 Remote Similarity NPC171639
0.6349 Remote Similarity NPC472828
0.6349 Remote Similarity NPC476679
0.6271 Remote Similarity NPC229403
0.625 Remote Similarity NPC246165
0.622 Remote Similarity NPC75810
0.622 Remote Similarity NPC24733
0.6212 Remote Similarity NPC267626
0.6212 Remote Similarity NPC49575
0.6212 Remote Similarity NPC474415
0.6212 Remote Similarity NPC475696
0.6212 Remote Similarity NPC474457
0.6212 Remote Similarity NPC474528
0.6212 Remote Similarity NPC55004
0.6207 Remote Similarity NPC51762
0.6207 Remote Similarity NPC60556
0.6207 Remote Similarity NPC166362
0.6207 Remote Similarity NPC474118
0.6207 Remote Similarity NPC109813
0.6207 Remote Similarity NPC86538
0.6207 Remote Similarity NPC227670
0.6207 Remote Similarity NPC141777
0.6173 Remote Similarity NPC21667
0.6154 Remote Similarity NPC470893
0.6154 Remote Similarity NPC123194
0.6119 Remote Similarity NPC231129
0.6119 Remote Similarity NPC469769
0.6104 Remote Similarity NPC174803
0.6104 Remote Similarity NPC259989
0.6102 Remote Similarity NPC248411
0.6066 Remote Similarity NPC124851
0.6029 Remote Similarity NPC474454
0.6029 Remote Similarity NPC474420
0.6029 Remote Similarity NPC475716
0.6029 Remote Similarity NPC82919
0.6029 Remote Similarity NPC474455
0.6029 Remote Similarity NPC5698
0.6024 Remote Similarity NPC152684
0.6024 Remote Similarity NPC147513
0.6 Remote Similarity NPC296337
0.6 Remote Similarity NPC145715
0.6 Remote Similarity NPC86683
0.597 Remote Similarity NPC470370
0.597 Remote Similarity NPC230823
0.597 Remote Similarity NPC278550
0.597 Remote Similarity NPC470369
0.5968 Remote Similarity NPC17518
0.5968 Remote Similarity NPC22765
0.5955 Remote Similarity NPC272732
0.5955 Remote Similarity NPC311164
0.5952 Remote Similarity NPC166458
0.5952 Remote Similarity NPC157479
0.5946 Remote Similarity NPC138409
0.5946 Remote Similarity NPC472831
0.5946 Remote Similarity NPC184919
0.5942 Remote Similarity NPC323153
0.5942 Remote Similarity NPC25853
0.5942 Remote Similarity NPC252809
0.5915 Remote Similarity NPC473959
0.5915 Remote Similarity NPC476559
0.5882 Remote Similarity NPC30215
0.5882 Remote Similarity NPC266295
0.5882 Remote Similarity NPC94991
0.5873 Remote Similarity NPC476681
0.5862 Remote Similarity NPC473614
0.5854 Remote Similarity NPC39966
0.5833 Remote Similarity NPC311769
0.5833 Remote Similarity NPC187619
0.5833 Remote Similarity NPC183422
0.5833 Remote Similarity NPC182106
0.5821 Remote Similarity NPC318036
0.5818 Remote Similarity NPC92224
0.5797 Remote Similarity NPC469321
0.5797 Remote Similarity NPC259261
0.5797 Remote Similarity NPC28755
0.5797 Remote Similarity NPC309825
0.5797 Remote Similarity NPC152211
0.5781 Remote Similarity NPC471681
0.5775 Remote Similarity NPC472544
0.5775 Remote Similarity NPC474480
0.5775 Remote Similarity NPC474596
0.5763 Remote Similarity NPC177470
0.5747 Remote Similarity NPC249312
0.5738 Remote Similarity NPC114239
0.5738 Remote Similarity NPC181141
0.5738 Remote Similarity NPC13991
0.5738 Remote Similarity NPC241784
0.5735 Remote Similarity NPC173815
0.5714 Remote Similarity NPC471867
0.5714 Remote Similarity NPC47840
0.5714 Remote Similarity NPC234264
0.5696 Remote Similarity NPC476308
0.5694 Remote Similarity NPC476682
0.5694 Remote Similarity NPC140233
0.5694 Remote Similarity NPC473902
0.5694 Remote Similarity NPC287744
0.5682 Remote Similarity NPC84171
0.5676 Remote Similarity NPC136813
0.5663 Remote Similarity NPC224072
0.5652 Remote Similarity NPC324944
0.5638 Remote Similarity NPC118275
0.5634 Remote Similarity NPC210346
0.5634 Remote Similarity NPC274704
0.5634 Remote Similarity NPC475795
0.5632 Remote Similarity NPC259252
0.5625 Remote Similarity NPC201713
0.5616 Remote Similarity NPC477009
0.5616 Remote Similarity NPC238352
0.5614 Remote Similarity NPC297643
0.5614 Remote Similarity NPC139717
0.5614 Remote Similarity NPC229262
0.5614 Remote Similarity NPC266298
0.5606 Remote Similarity NPC474416
0.5606 Remote Similarity NPC127944
0.56 Remote Similarity NPC167527

  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 NPC472830 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
0.6081 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6081 Remote Similarity NPD6939 Phase 2
0.5789 Remote Similarity NPD5365 Phase 2
0.5647 Remote Similarity NPD2208 Approved
0.5647 Remote Similarity NPD2205 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