Structure

Physi-Chem Properties

Molecular Weight:  222.16
Volume:  239.975
LogP:  3.063
LogD:  2.494
LogS:  -2.042
# Rotatable Bonds:  0
TPSA:  32.76
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.505
Synthetic Accessibility Score:  4.899
Fsp3:  0.857
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.486
MDCK Permeability:  1.867516948550474e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.02
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.354
Plasma Protein Binding (PPB):  53.388275146484375%
Volume Distribution (VD):  1.373
Pgp-substrate:  43.84547424316406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.029
CYP1A2-substrate:  0.404
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.862
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.076
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.393
CYP3A4-inhibitor:  0.399
CYP3A4-substrate:  0.469

ADMET: Excretion

Clearance (CL):  14.214
Half-life (T1/2):  0.305

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.339
Drug-inuced Liver Injury (DILI):  0.253
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.308
Maximum Recommended Daily Dose:  0.657
Skin Sensitization:  0.671
Carcinogencity:  0.876
Eye Corrosion:  0.924
Eye Irritation:  0.918
Respiratory Toxicity:  0.935

Download Data

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

  Natural Product: NPC50435

Natural Product ID:  NPC50435
Common Name*:   Nanonorcaryophyllene A
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FDXOLTKNPDKRPV-PEDHHIEDSA-N
Standard InCHI:  InChI=1S/C14H22O2/c1-9-4-5-12-14(3,16-12)7-6-11-10(9)8-13(11,2)15/h10-12,15H,1,4-8H2,2-3H3/t10-,11-,12-,13-,14-/m0/s1
SMILES:  C=C1CC[C@H]2[C@](C)(CC[C@H]3[C@H]1C[C@]3(C)O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL442685
PubChem CID:   11276101
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO22870 Sinularia nanolobata Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[15104488]
NPO22870 Sinularia nanolobata Species Alcyoniidae 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
NPT91 Cell Line KB Homo sapiens ED50 > 20.0 ug ml-1 PMID[529874]
NPT2356 Cell Line NCI-H661 Homo sapiens ED50 > 20.0 ug ml-1 PMID[529874]
NPT579 Cell Line DLD-1 Homo sapiens ED50 > 20.0 ug ml-1 PMID[529874]
NPT165 Cell Line HeLa Homo sapiens ED50 > 20.0 ug ml-1 PMID[529874]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 > 20.0 ug ml-1 PMID[529874]

☑ 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 NPC50435 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
0.85 High Similarity NPC101285
0.85 High Similarity NPC65786
0.85 High Similarity NPC7491
0.85 High Similarity NPC13789
0.85 High Similarity NPC27853
0.8462 Intermediate Similarity NPC33583
0.8462 Intermediate Similarity NPC161612
0.7857 Intermediate Similarity NPC329763
0.7705 Intermediate Similarity NPC286752
0.7647 Intermediate Similarity NPC259299
0.7536 Intermediate Similarity NPC305698
0.75 Intermediate Similarity NPC469328
0.746 Intermediate Similarity NPC24443
0.7429 Intermediate Similarity NPC74722
0.7429 Intermediate Similarity NPC304690
0.7361 Intermediate Similarity NPC476709
0.7273 Intermediate Similarity NPC40206
0.726 Intermediate Similarity NPC190859
0.72 Intermediate Similarity NPC471454
0.7188 Intermediate Similarity NPC210316
0.7162 Intermediate Similarity NPC36479
0.7123 Intermediate Similarity NPC143576
0.7105 Intermediate Similarity NPC52755
0.7105 Intermediate Similarity NPC477089
0.7101 Intermediate Similarity NPC61503
0.7101 Intermediate Similarity NPC471200
0.7067 Intermediate Similarity NPC293223
0.7067 Intermediate Similarity NPC170148
0.7067 Intermediate Similarity NPC329626
0.7031 Intermediate Similarity NPC223604
0.6974 Remote Similarity NPC476703
0.6949 Remote Similarity NPC87439
0.6944 Remote Similarity NPC239373
0.6944 Remote Similarity NPC329989
0.6933 Remote Similarity NPC474419
0.6933 Remote Similarity NPC12696
0.6901 Remote Similarity NPC269077
0.6901 Remote Similarity NPC253303
0.6866 Remote Similarity NPC310228
0.6866 Remote Similarity NPC52431
0.6857 Remote Similarity NPC250836
0.6857 Remote Similarity NPC300442
0.6842 Remote Similarity NPC268111
0.6812 Remote Similarity NPC473759
0.6812 Remote Similarity NPC473508
0.6812 Remote Similarity NPC474155
0.6806 Remote Similarity NPC245795
0.6806 Remote Similarity NPC266578
0.6769 Remote Similarity NPC67508
0.6769 Remote Similarity NPC84824
0.6757 Remote Similarity NPC306085
0.6753 Remote Similarity NPC84360
0.675 Remote Similarity NPC145963
0.6714 Remote Similarity NPC140233
0.6714 Remote Similarity NPC101128
0.6714 Remote Similarity NPC300593
0.6714 Remote Similarity NPC219940
0.6714 Remote Similarity NPC287744
0.6712 Remote Similarity NPC144647
0.6712 Remote Similarity NPC269841
0.6712 Remote Similarity NPC234511
0.6712 Remote Similarity NPC16964
0.6711 Remote Similarity NPC93213
0.6709 Remote Similarity NPC475946
0.6667 Remote Similarity NPC172622
0.6667 Remote Similarity NPC475980
0.6667 Remote Similarity NPC231601
0.6667 Remote Similarity NPC251335
0.6667 Remote Similarity NPC260852
0.6667 Remote Similarity NPC475807
0.6667 Remote Similarity NPC63111
0.6625 Remote Similarity NPC118116
0.6625 Remote Similarity NPC77003
0.6623 Remote Similarity NPC476607
0.6622 Remote Similarity NPC283316
0.6622 Remote Similarity NPC470041
0.6585 Remote Similarity NPC86238
0.6579 Remote Similarity NPC471525
0.6548 Remote Similarity NPC474765
0.6543 Remote Similarity NPC103171
0.6538 Remote Similarity NPC186109
0.6533 Remote Similarity NPC40327
0.6533 Remote Similarity NPC477084
0.6528 Remote Similarity NPC475897
0.6528 Remote Similarity NPC311736
0.6528 Remote Similarity NPC473929
0.6528 Remote Similarity NPC267027
0.6522 Remote Similarity NPC66020
0.6522 Remote Similarity NPC475412
0.6508 Remote Similarity NPC142103
0.65 Remote Similarity NPC76054
0.65 Remote Similarity NPC258965
0.65 Remote Similarity NPC156658
0.6494 Remote Similarity NPC475861
0.6479 Remote Similarity NPC144650
0.6479 Remote Similarity NPC476702
0.6471 Remote Similarity NPC475830
0.6471 Remote Similarity NPC152438
0.6471 Remote Similarity NPC240206
0.6471 Remote Similarity NPC41180
0.6463 Remote Similarity NPC5958
0.6463 Remote Similarity NPC239308
0.6462 Remote Similarity NPC165755
0.6462 Remote Similarity NPC161473
0.6452 Remote Similarity NPC100445
0.6447 Remote Similarity NPC95165
0.6438 Remote Similarity NPC82337
0.6438 Remote Similarity NPC472255
0.6438 Remote Similarity NPC139207
0.6438 Remote Similarity NPC472253
0.6438 Remote Similarity NPC185874
0.6438 Remote Similarity NPC73603
0.6438 Remote Similarity NPC163290
0.6429 Remote Similarity NPC225342
0.6429 Remote Similarity NPC470242
0.6429 Remote Similarity NPC15152
0.642 Remote Similarity NPC471661
0.6418 Remote Similarity NPC264779
0.6418 Remote Similarity NPC39068
0.6418 Remote Similarity NPC170780
0.641 Remote Similarity NPC236228
0.641 Remote Similarity NPC256720
0.641 Remote Similarity NPC271070
0.641 Remote Similarity NPC472472
0.6406 Remote Similarity NPC474331
0.64 Remote Similarity NPC129630
0.64 Remote Similarity NPC471781
0.6395 Remote Similarity NPC161560
0.6389 Remote Similarity NPC469326
0.6389 Remote Similarity NPC11555
0.6389 Remote Similarity NPC258595
0.6389 Remote Similarity NPC208198
0.6389 Remote Similarity NPC2728
0.6389 Remote Similarity NPC172613
0.6389 Remote Similarity NPC60837
0.6389 Remote Similarity NPC261782
0.6389 Remote Similarity NPC165069
0.6389 Remote Similarity NPC205618
0.6389 Remote Similarity NPC282619
0.6377 Remote Similarity NPC143810
0.6377 Remote Similarity NPC83838
0.6377 Remote Similarity NPC475931
0.6377 Remote Similarity NPC99480
0.6377 Remote Similarity NPC122239
0.6377 Remote Similarity NPC184049
0.6375 Remote Similarity NPC476701
0.6375 Remote Similarity NPC80999
0.6364 Remote Similarity NPC71152
0.6351 Remote Similarity NPC244790
0.6351 Remote Similarity NPC470040
0.6351 Remote Similarity NPC276616
0.6333 Remote Similarity NPC15162
0.6324 Remote Similarity NPC278550
0.6316 Remote Similarity NPC41886
0.6316 Remote Similarity NPC469343
0.631 Remote Similarity NPC471379
0.631 Remote Similarity NPC47958
0.631 Remote Similarity NPC304509
0.631 Remote Similarity NPC196911
0.631 Remote Similarity NPC149725
0.6308 Remote Similarity NPC35519
0.6308 Remote Similarity NPC181255
0.6308 Remote Similarity NPC306195
0.6308 Remote Similarity NPC157781
0.6308 Remote Similarity NPC179169
0.6301 Remote Similarity NPC272125
0.6301 Remote Similarity NPC476406
0.6296 Remote Similarity NPC474739
0.6286 Remote Similarity NPC99487
0.6286 Remote Similarity NPC162109
0.6286 Remote Similarity NPC127824
0.6286 Remote Similarity NPC469694
0.6286 Remote Similarity NPC240506
0.6282 Remote Similarity NPC23231
0.6282 Remote Similarity NPC60818
0.6282 Remote Similarity NPC113639
0.6267 Remote Similarity NPC474248
0.6267 Remote Similarity NPC329656
0.6267 Remote Similarity NPC9942
0.6265 Remote Similarity NPC477978
0.6265 Remote Similarity NPC471340
0.6265 Remote Similarity NPC475842
0.625 Remote Similarity NPC68656
0.625 Remote Similarity NPC264610
0.625 Remote Similarity NPC309300
0.625 Remote Similarity NPC131623
0.625 Remote Similarity NPC91251
0.625 Remote Similarity NPC3852
0.625 Remote Similarity NPC225415
0.625 Remote Similarity NPC329773
0.625 Remote Similarity NPC199937
0.6235 Remote Similarity NPC322922
0.6235 Remote Similarity NPC321812
0.6235 Remote Similarity NPC255143
0.6235 Remote Similarity NPC475684
0.6234 Remote Similarity NPC477085
0.6234 Remote Similarity NPC92909
0.6234 Remote Similarity NPC107783
0.6234 Remote Similarity NPC310608
0.6232 Remote Similarity NPC189290

  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 NPC50435 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
0.6286 Remote Similarity NPD1145 Discontinued
0.6197 Remote Similarity NPD368 Approved
0.6129 Remote Similarity NPD388 Approved
0.6129 Remote Similarity NPD386 Approved
0.6094 Remote Similarity NPD9410 Clinical (unspecified phase)
0.6071 Remote Similarity NPD6695 Phase 3
0.6 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5955 Remote Similarity NPD3168 Discontinued
0.5949 Remote Similarity NPD6926 Approved
0.5949 Remote Similarity NPD6924 Approved
0.5946 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5904 Remote Similarity NPD6930 Phase 2
0.5904 Remote Similarity NPD6931 Approved
0.5811 Remote Similarity NPD371 Approved
0.5802 Remote Similarity NPD6933 Approved
0.5797 Remote Similarity NPD342 Phase 1
0.5795 Remote Similarity NPD7750 Discontinued
0.5795 Remote Similarity NPD7524 Approved
0.5783 Remote Similarity NPD6929 Approved
0.5781 Remote Similarity NPD385 Approved
0.5781 Remote Similarity NPD384 Approved
0.5778 Remote Similarity NPD7838 Discovery
0.5732 Remote Similarity NPD6932 Approved
0.5667 Remote Similarity NPD1695 Approved
0.561 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5604 Remote Similarity NPD46 Approved
0.5604 Remote Similarity NPD6698 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