Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  335.374
LogP:  5.378
LogD:  4.903
LogS:  -5.946
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.462
Synthetic Accessibility Score:  3.603
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.73
MDCK Permeability:  2.6121373593923636e-05
Pgp-inhibitor:  0.157
Pgp-substrate:  0.015
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.028
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.157
Plasma Protein Binding (PPB):  96.5708236694336%
Volume Distribution (VD):  2.035
Pgp-substrate:  1.169201135635376%

ADMET: Metabolism

CYP1A2-inhibitor:  0.288
CYP1A2-substrate:  0.538
CYP2C19-inhibitor:  0.276
CYP2C19-substrate:  0.741
CYP2C9-inhibitor:  0.392
CYP2C9-substrate:  0.949
CYP2D6-inhibitor:  0.769
CYP2D6-substrate:  0.872
CYP3A4-inhibitor:  0.565
CYP3A4-substrate:  0.219

ADMET: Excretion

Clearance (CL):  2.552
Half-life (T1/2):  0.233

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.113
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.848
Skin Sensitization:  0.916
Carcinogencity:  0.028
Eye Corrosion:  0.007
Eye Irritation:  0.15
Respiratory Toxicity:  0.027

Download Data

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

  Natural Product: NPC266298

Natural Product ID:  NPC266298
Common Name*:   Cembrene-C
IUPAC Name:   (1E,3E,7E,11E)-1,7,11-trimethyl-4-propan-2-ylcyclotetradeca-1,3,7,11-tetraene
Synonyms:  
Standard InCHIKey:  UJUWZMUCEGGBOH-YBJPMODXSA-N
Standard InCHI:  InChI=1S/C20H32/c1-16(2)20-14-12-18(4)10-6-8-17(3)9-7-11-19(5)13-15-20/h8,11-12,14,16H,6-7,9-10,13,15H2,1-5H3/b17-8+,18-12+,19-11+,20-14+
SMILES:  C/C/1=CCC/C(=C/CC/C(=C/C=C(CC1)/C(C)C)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2414202
PubChem CID:   6521442
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0000008] Cembrane diterpenoids

*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
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[10923847]
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[23859780]
NPO20809 Sarcophyton trocheliophorum 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
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 26600.0 nM PMID[457137]

☑ 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 NPC266298 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
0.8919 High Similarity NPC239039
0.8889 High Similarity NPC92224
0.8378 Intermediate Similarity NPC282119
0.8286 Intermediate Similarity NPC471327
0.825 Intermediate Similarity NPC218918
0.825 Intermediate Similarity NPC120926
0.825 Intermediate Similarity NPC144023
0.8049 Intermediate Similarity NPC177470
0.8 Intermediate Similarity NPC183670
0.7838 Intermediate Similarity NPC173592
0.7838 Intermediate Similarity NPC99088
0.7838 Intermediate Similarity NPC305759
0.7778 Intermediate Similarity NPC206088
0.7714 Intermediate Similarity NPC115959
0.7714 Intermediate Similarity NPC123965
0.7692 Intermediate Similarity NPC190810
0.7692 Intermediate Similarity NPC34764
0.7692 Intermediate Similarity NPC76145
0.7568 Intermediate Similarity NPC213749
0.75 Intermediate Similarity NPC229262
0.75 Intermediate Similarity NPC48638
0.75 Intermediate Similarity NPC49088
0.75 Intermediate Similarity NPC139717
0.75 Intermediate Similarity NPC45727
0.75 Intermediate Similarity NPC60288
0.75 Intermediate Similarity NPC297643
0.7391 Intermediate Similarity NPC17810
0.7333 Intermediate Similarity NPC323445
0.7297 Intermediate Similarity NPC3649
0.7297 Intermediate Similarity NPC151719
0.7297 Intermediate Similarity NPC100879
0.7222 Intermediate Similarity NPC138113
0.7222 Intermediate Similarity NPC34671
0.7209 Intermediate Similarity NPC473912
0.7174 Intermediate Similarity NPC124851
0.7045 Intermediate Similarity NPC109813
0.7045 Intermediate Similarity NPC86538
0.7045 Intermediate Similarity NPC60556
0.7021 Intermediate Similarity NPC17518
0.7021 Intermediate Similarity NPC22765
0.6944 Remote Similarity NPC138325
0.6944 Remote Similarity NPC64176
0.6944 Remote Similarity NPC288991
0.6944 Remote Similarity NPC262789
0.6939 Remote Similarity NPC208638
0.6889 Remote Similarity NPC202189
0.6889 Remote Similarity NPC248411
0.6875 Remote Similarity NPC329773
0.6875 Remote Similarity NPC26960
0.6875 Remote Similarity NPC182102
0.6863 Remote Similarity NPC470893
0.6863 Remote Similarity NPC329686
0.6842 Remote Similarity NPC66577
0.68 Remote Similarity NPC476679
0.675 Remote Similarity NPC182392
0.6739 Remote Similarity NPC86683
0.6739 Remote Similarity NPC13991
0.6739 Remote Similarity NPC296337
0.6739 Remote Similarity NPC241784
0.6739 Remote Similarity NPC114239
0.6596 Remote Similarity NPC8610
0.6596 Remote Similarity NPC262558
0.6538 Remote Similarity NPC188789
0.6486 Remote Similarity NPC179103
0.6486 Remote Similarity NPC76765
0.6481 Remote Similarity NPC469769
0.6471 Remote Similarity NPC45283
0.6327 Remote Similarity NPC106990
0.625 Remote Similarity NPC176621
0.6226 Remote Similarity NPC223604
0.6226 Remote Similarity NPC469770
0.6222 Remote Similarity NPC188596
0.6216 Remote Similarity NPC10183
0.617 Remote Similarity NPC138935
0.6122 Remote Similarity NPC178644
0.6111 Remote Similarity NPC88325
0.6111 Remote Similarity NPC249645
0.6111 Remote Similarity NPC55412
0.6111 Remote Similarity NPC4881
0.6111 Remote Similarity NPC96663
0.6098 Remote Similarity NPC62779
0.6087 Remote Similarity NPC105246
0.6087 Remote Similarity NPC190232
0.6078 Remote Similarity NPC214584
0.6078 Remote Similarity NPC26906
0.6078 Remote Similarity NPC27438
0.6071 Remote Similarity NPC475716
0.6042 Remote Similarity NPC24824
0.6042 Remote Similarity NPC165651
0.6042 Remote Similarity NPC210560
0.6034 Remote Similarity NPC155849
0.6 Remote Similarity NPC281986
0.6 Remote Similarity NPC227632
0.6 Remote Similarity NPC246165
0.6 Remote Similarity NPC196831
0.6 Remote Similarity NPC62086
0.6 Remote Similarity NPC208749
0.6 Remote Similarity NPC321568
0.6 Remote Similarity NPC11130
0.6 Remote Similarity NPC230823
0.6 Remote Similarity NPC22019
0.6 Remote Similarity NPC78551
0.5965 Remote Similarity NPC127824
0.5962 Remote Similarity NPC68014
0.5962 Remote Similarity NPC294358
0.5962 Remote Similarity NPC306195
0.5962 Remote Similarity NPC35519
0.5962 Remote Similarity NPC157781
0.5962 Remote Similarity NPC179169
0.5962 Remote Similarity NPC181255
0.5962 Remote Similarity NPC71506
0.5962 Remote Similarity NPC473728
0.5962 Remote Similarity NPC177112
0.5962 Remote Similarity NPC40417
0.5957 Remote Similarity NPC192529
0.5957 Remote Similarity NPC106819
0.5946 Remote Similarity NPC31891
0.5946 Remote Similarity NPC287191
0.5946 Remote Similarity NPC266144
0.5946 Remote Similarity NPC266539
0.5926 Remote Similarity NPC281590
0.5926 Remote Similarity NPC123194
0.5926 Remote Similarity NPC474644
0.5918 Remote Similarity NPC22098
0.5918 Remote Similarity NPC195246
0.5918 Remote Similarity NPC159420
0.5918 Remote Similarity NPC276009
0.5909 Remote Similarity NPC180840
0.5893 Remote Similarity NPC181872
0.5882 Remote Similarity NPC200129
0.5882 Remote Similarity NPC32351
0.587 Remote Similarity NPC269823
0.587 Remote Similarity NPC469969
0.587 Remote Similarity NPC103290
0.587 Remote Similarity NPC473614
0.5862 Remote Similarity NPC469728
0.5854 Remote Similarity NPC13217
0.5849 Remote Similarity NPC69898
0.5849 Remote Similarity NPC295777
0.5849 Remote Similarity NPC268564
0.5833 Remote Similarity NPC308844
0.5818 Remote Similarity NPC473865
0.5818 Remote Similarity NPC474643
0.58 Remote Similarity NPC91962
0.5789 Remote Similarity NPC5698
0.5789 Remote Similarity NPC475931
0.5789 Remote Similarity NPC143834
0.5789 Remote Similarity NPC122239
0.5769 Remote Similarity NPC244038
0.5763 Remote Similarity NPC474086
0.5745 Remote Similarity NPC68889
0.5745 Remote Similarity NPC213538
0.5745 Remote Similarity NPC256766
0.5745 Remote Similarity NPC67761
0.5745 Remote Similarity NPC88079
0.5745 Remote Similarity NPC209279
0.5745 Remote Similarity NPC194586
0.5745 Remote Similarity NPC193180
0.5745 Remote Similarity NPC108494
0.5745 Remote Similarity NPC51758
0.5745 Remote Similarity NPC180871
0.5741 Remote Similarity NPC202850
0.5741 Remote Similarity NPC63396
0.5738 Remote Similarity NPC149680
0.5714 Remote Similarity NPC49575
0.5714 Remote Similarity NPC55004
0.5714 Remote Similarity NPC475696
0.5714 Remote Similarity NPC52012
0.5714 Remote Similarity NPC276825
0.5714 Remote Similarity NPC474415
0.5714 Remote Similarity NPC474528
0.5714 Remote Similarity NPC474457
0.5714 Remote Similarity NPC267626
0.569 Remote Similarity NPC323153
0.569 Remote Similarity NPC471081
0.569 Remote Similarity NPC252809
0.5686 Remote Similarity NPC234597
0.5682 Remote Similarity NPC201753
0.5682 Remote Similarity NPC185839
0.5676 Remote Similarity NPC38513
0.5676 Remote Similarity NPC172053
0.5667 Remote Similarity NPC226066
0.5667 Remote Similarity NPC4638
0.5667 Remote Similarity NPC476559
0.566 Remote Similarity NPC471751
0.5645 Remote Similarity NPC278895
0.5636 Remote Similarity NPC477984
0.5636 Remote Similarity NPC297280
0.5636 Remote Similarity NPC297020
0.5636 Remote Similarity NPC275472
0.5625 Remote Similarity NPC227670
0.5625 Remote Similarity NPC166362
0.5625 Remote Similarity NPC23145
0.5625 Remote Similarity NPC116934
0.5625 Remote Similarity NPC474118
0.5625 Remote Similarity NPC51762
0.5625 Remote Similarity NPC301972
0.5625 Remote Similarity NPC90506
0.5625 Remote Similarity NPC141777
0.5625 Remote Similarity NPC15162

  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 NPC266298 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
0.7692 Intermediate Similarity NPD319 Phase 1
0.7391 Intermediate Similarity NPD8262 Approved
0.6136 Remote Similarity NPD5783 Phase 3
0.6111 Remote Similarity NPD4219 Approved
0.6087 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5667 Remote Similarity NPD5325 Clinical (unspecified phase)

  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