Structure

Physi-Chem Properties

Molecular Weight:  582.16
Volume:  528.868
LogP:  -0.088
LogD:  -0.232
LogS:  -3.799
# Rotatable Bonds:  7
TPSA:  227.2
# H-Bond Aceptor:  15
# H-Bond Donor:  7
# Rings:  5
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.154
Synthetic Accessibility Score:  4.649
Fsp3:  0.5
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.342
MDCK Permeability:  3.179413397447206e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.827
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.164
Plasma Protein Binding (PPB):  69.12979125976562%
Volume Distribution (VD):  0.67
Pgp-substrate:  20.51624298095703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.935
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.362
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.22
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.203
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  1.21
Half-life (T1/2):  0.555

ADMET: Toxicity

hERG Blockers:  0.468
Human Hepatotoxicity (H-HT):  0.103
Drug-inuced Liver Injury (DILI):  0.947
AMES Toxicity:  0.732
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.753
Carcinogencity:  0.176
Eye Corrosion:  0.003
Eye Irritation:  0.066
Respiratory Toxicity:  0.022

Download Data

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

  Natural Product: NPC51762

Natural Product ID:  NPC51762
Common Name*:   UEHKTJFOLYEULK-YXJLRHLOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UEHKTJFOLYEULK-YXJLRHLOSA-N
Standard InCHI:  InChI=1S/C15H24/c1-9(2)13-12-7-8-15(12,4)11-6-5-10(3)14(11)13/h10-14H,1,5-8H2,2-4H3/t10-,11+,12+,13-,14-,15-/m1/s1
SMILES:  C[C@@H]1CC[C@H]2[C@@H]1[C@H](C(=C)C)[C@H]1[C@]2(C)CC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL400313
PubChem CID:   10726904
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001565] Iridoids 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

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. formosan soft coral n.a. PMID[17845002]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[24370010]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[9722490]
NPO13916 Nephthea erecta Species Nephtheidae 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
NPT139 Cell Line HT-29 Homo sapiens ED50 = 3.2 ug ml-1 PMID[486328]
NPT168 Cell Line P388 Mus musculus ED50 = 2.8 ug ml-1 PMID[486328]
NPT139 Cell Line HT-29 Homo sapiens ED50 = 3.2 ug ml-1 PMID[486329]
NPT168 Cell Line P388 Mus musculus ED50 = 2.8 ug ml-1 PMID[486329]

☑ 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 NPC51762 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 NPC474118
0.95 High Similarity NPC473614
0.9048 High Similarity NPC227670
0.9048 High Similarity NPC141777
0.9048 High Similarity NPC166362
0.8636 High Similarity NPC229403
0.8333 Intermediate Similarity NPC246165
0.8182 Intermediate Similarity NPC90506
0.8182 Intermediate Similarity NPC23145
0.8182 Intermediate Similarity NPC90803
0.7907 Intermediate Similarity NPC227632
0.7907 Intermediate Similarity NPC62086
0.7907 Intermediate Similarity NPC78551
0.7872 Intermediate Similarity NPC178644
0.7826 Intermediate Similarity NPC49088
0.7755 Intermediate Similarity NPC471681
0.766 Intermediate Similarity NPC323445
0.7551 Intermediate Similarity NPC200129
0.7391 Intermediate Similarity NPC60556
0.7391 Intermediate Similarity NPC109813
0.7174 Intermediate Similarity NPC473912
0.7143 Intermediate Similarity NPC162109
0.7018 Intermediate Similarity NPC15152
0.6957 Remote Similarity NPC103290
0.6809 Remote Similarity NPC193180
0.6809 Remote Similarity NPC105246
0.6809 Remote Similarity NPC190232
0.6792 Remote Similarity NPC127944
0.6735 Remote Similarity NPC241784
0.6735 Remote Similarity NPC13991
0.6735 Remote Similarity NPC114239
0.6667 Remote Similarity NPC86538
0.6552 Remote Similarity NPC47840
0.6552 Remote Similarity NPC234264
0.6545 Remote Similarity NPC123194
0.6531 Remote Similarity NPC248411
0.6441 Remote Similarity NPC147524
0.64 Remote Similarity NPC296337
0.64 Remote Similarity NPC86683
0.6333 Remote Similarity NPC124112
0.6316 Remote Similarity NPC55004
0.6316 Remote Similarity NPC49575
0.6316 Remote Similarity NPC267626
0.6271 Remote Similarity NPC270042
0.625 Remote Similarity NPC470893
0.625 Remote Similarity NPC10183
0.623 Remote Similarity NPC475704
0.6207 Remote Similarity NPC472830
0.6207 Remote Similarity NPC469769
0.6154 Remote Similarity NPC124851
0.6122 Remote Similarity NPC177470
0.6102 Remote Similarity NPC184049
0.6102 Remote Similarity NPC5698
0.6102 Remote Similarity NPC99480
0.6102 Remote Similarity NPC309825
0.6071 Remote Similarity NPC286752
0.6038 Remote Similarity NPC17518
0.6038 Remote Similarity NPC22765
0.6034 Remote Similarity NPC230823
0.6032 Remote Similarity NPC135650
0.6032 Remote Similarity NPC176171
0.6032 Remote Similarity NPC162309
0.6 Remote Similarity NPC25853
0.6 Remote Similarity NPC323153
0.6 Remote Similarity NPC192529
0.6 Remote Similarity NPC252809
0.5957 Remote Similarity NPC229262
0.5957 Remote Similarity NPC297643
0.5957 Remote Similarity NPC139717
0.5938 Remote Similarity NPC308522
0.5938 Remote Similarity NPC74885
0.5932 Remote Similarity NPC94991
0.5932 Remote Similarity NPC30215
0.5932 Remote Similarity NPC266295
0.5926 Remote Similarity NPC476681
0.5918 Remote Similarity NPC120926
0.5918 Remote Similarity NPC218918
0.5918 Remote Similarity NPC144023
0.5882 Remote Similarity NPC202189
0.587 Remote Similarity NPC92224
0.5833 Remote Similarity NPC259261
0.5818 Remote Similarity NPC236623
0.5806 Remote Similarity NPC474086
0.5806 Remote Similarity NPC165695
0.5806 Remote Similarity NPC474480
0.5763 Remote Similarity NPC7491
0.5763 Remote Similarity NPC27853
0.5763 Remote Similarity NPC278550
0.5763 Remote Similarity NPC13789
0.5763 Remote Similarity NPC101285
0.5763 Remote Similarity NPC65786
0.5745 Remote Similarity NPC34764
0.5745 Remote Similarity NPC76145
0.5745 Remote Similarity NPC190810
0.5738 Remote Similarity NPC135648
0.5714 Remote Similarity NPC472472
0.5714 Remote Similarity NPC310643
0.5714 Remote Similarity NPC287744
0.5714 Remote Similarity NPC183670
0.5714 Remote Similarity NPC140233
0.5714 Remote Similarity NPC219940
0.5714 Remote Similarity NPC473902
0.5672 Remote Similarity NPC133873
0.566 Remote Similarity NPC40249
0.566 Remote Similarity NPC131981
0.566 Remote Similarity NPC173996
0.5645 Remote Similarity NPC475795
0.5645 Remote Similarity NPC213152
0.5645 Remote Similarity NPC210346
0.5625 Remote Similarity NPC238352
0.5625 Remote Similarity NPC183422
0.5625 Remote Similarity NPC477009
0.5625 Remote Similarity NPC239039
0.5625 Remote Similarity NPC266298
0.5625 Remote Similarity NPC187619
0.5625 Remote Similarity NPC300442
0.5614 Remote Similarity NPC474416

  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 NPC51762 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
0.6809 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5745 Remote Similarity NPD319 Phase 1
0.566 Remote Similarity NPD343 Approved
0.566 Remote Similarity NPD344 Approved
0.566 Remote Similarity NPD345 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