Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  335.374
LogP:  6.562
LogD:  5.305
LogS:  -6.593
# 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:  3.84
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.759
MDCK Permeability:  1.9154860638082027e-05
Pgp-inhibitor:  0.875
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.046
20% Bioavailability (F20%):  0.091
30% Bioavailability (F30%):  0.061

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.227
Plasma Protein Binding (PPB):  96.27340698242188%
Volume Distribution (VD):  1.148
Pgp-substrate:  0.853017270565033%

ADMET: Metabolism

CYP1A2-inhibitor:  0.432
CYP1A2-substrate:  0.403
CYP2C19-inhibitor:  0.333
CYP2C19-substrate:  0.15
CYP2C9-inhibitor:  0.375
CYP2C9-substrate:  0.934
CYP2D6-inhibitor:  0.57
CYP2D6-substrate:  0.869
CYP3A4-inhibitor:  0.444
CYP3A4-substrate:  0.151

ADMET: Excretion

Clearance (CL):  3.691
Half-life (T1/2):  0.277

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.104
Drug-inuced Liver Injury (DILI):  0.013
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.913
Skin Sensitization:  0.963
Carcinogencity:  0.017
Eye Corrosion:  0.961
Eye Irritation:  0.955
Respiratory Toxicity:  0.018

Download Data

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

  Natural Product: NPC92224

Natural Product ID:  NPC92224
Common Name*:   Cembrene_A
IUPAC Name:   (1E,5E,9E,12R)-1,5,9-trimethyl-12-prop-1-en-2-ylcyclotetradeca-1,5,9-triene
Synonyms:   Cembrene A
Standard InCHIKey:  VWSPQDDPRITBAM-KPGNMOGWSA-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/h8,11-12,20H,1,6-7,9-10,13-15H2,2-5H3/b17-8+,18-12+,19-11+/t20-/m0/s1
SMILES:  C/C/1=CC[C@@H](CC/C(=C/CC/C(=C/CC1)/C)/C)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL518765
PubChem CID:   5281384
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
NPO24464 Nephthea brassica Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[10579864]
NPO15264 Garcinia paucinervis Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20594858]
NPO27927 Alligator sinensis Species Alligatoridae Eukaryota n.a. n.a. n.a. PMID[9287418]
NPO27927 Alligator sinensis Species Alligatoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15264 Garcinia paucinervis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24464 Nephthea brassica 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
NPT168 Cell Line P388 Mus musculus ED50 = 1.1 ug ml-1 PMID[506611]
NPT81 Cell Line A549 Homo sapiens ED50 = 1.11 ug ml-1 PMID[506611]
NPT139 Cell Line HT-29 Homo sapiens ED50 = 3.42 ug ml-1 PMID[506611]
NPT91 Cell Line KB Homo sapiens ED50 = 3.73 ug ml-1 PMID[506611]
NPT545 Individual Protein Phospholipase A2 group 1B Homo sapiens Activity = 5.0 % PMID[506612]
NPT545 Individual Protein Phospholipase A2 group 1B Homo sapiens Activity = 45.0 % PMID[506612]
NPT4137 Cell Line Splenocytes Mus musculus CC50 = 21200.0 nM PMID[506614]
NPT4137 Cell Line Splenocytes Mus musculus IC50 = 44300.0 nM PMID[506614]
NPT4137 Cell Line Splenocytes Mus musculus IC50 = 16700.0 nM PMID[506614]
NPT2 Others Unspecified Ratio CC50/IC50 = 0.5 n.a. PMID[506614]
NPT2 Others Unspecified Ratio CC50/IC50 = 1.3 n.a. PMID[506614]

☑ 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 NPC92224 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
0.8889 High Similarity NPC266298
0.8788 High Similarity NPC471327
0.8611 High Similarity NPC34764
0.8611 High Similarity NPC76145
0.8611 High Similarity NPC190810
0.8378 Intermediate Similarity NPC139717
0.8378 Intermediate Similarity NPC229262
0.8378 Intermediate Similarity NPC297643
0.8333 Intermediate Similarity NPC282119
0.8235 Intermediate Similarity NPC206088
0.8182 Intermediate Similarity NPC115959
0.8182 Intermediate Similarity NPC123965
0.8 Intermediate Similarity NPC213749
0.7949 Intermediate Similarity NPC183670
0.7895 Intermediate Similarity NPC239039
0.7857 Intermediate Similarity NPC49088
0.775 Intermediate Similarity NPC144023
0.775 Intermediate Similarity NPC120926
0.775 Intermediate Similarity NPC218918
0.7714 Intermediate Similarity NPC3649
0.7714 Intermediate Similarity NPC100879
0.7714 Intermediate Similarity NPC151719
0.7674 Intermediate Similarity NPC323445
0.7647 Intermediate Similarity NPC34671
0.7561 Intermediate Similarity NPC177470
0.7561 Intermediate Similarity NPC473912
0.75 Intermediate Similarity NPC124851
0.7436 Intermediate Similarity NPC48638
0.7436 Intermediate Similarity NPC45727
0.7381 Intermediate Similarity NPC60556
0.7381 Intermediate Similarity NPC86538
0.7381 Intermediate Similarity NPC109813
0.7353 Intermediate Similarity NPC138325
0.7333 Intermediate Similarity NPC17518
0.7333 Intermediate Similarity NPC22765
0.7297 Intermediate Similarity NPC305759
0.7297 Intermediate Similarity NPC173592
0.7297 Intermediate Similarity NPC99088
0.7222 Intermediate Similarity NPC66577
0.7209 Intermediate Similarity NPC248411
0.7209 Intermediate Similarity NPC202189
0.7174 Intermediate Similarity NPC329773
0.7174 Intermediate Similarity NPC26960
0.7174 Intermediate Similarity NPC182102
0.7143 Intermediate Similarity NPC138113
0.7105 Intermediate Similarity NPC182392
0.7045 Intermediate Similarity NPC114239
0.7045 Intermediate Similarity NPC13991
0.7045 Intermediate Similarity NPC296337
0.7045 Intermediate Similarity NPC241784
0.7045 Intermediate Similarity NPC86683
0.6957 Remote Similarity NPC17810
0.6944 Remote Similarity NPC60288
0.6905 Remote Similarity NPC188596
0.6889 Remote Similarity NPC8610
0.6889 Remote Similarity NPC262558
0.6875 Remote Similarity NPC208638
0.6857 Remote Similarity NPC76765
0.6857 Remote Similarity NPC179103
0.6667 Remote Similarity NPC210560
0.6667 Remote Similarity NPC24824
0.6667 Remote Similarity NPC165651
0.6596 Remote Similarity NPC106990
0.6571 Remote Similarity NPC10183
0.6522 Remote Similarity NPC195246
0.6522 Remote Similarity NPC22098
0.6522 Remote Similarity NPC276009
0.6471 Remote Similarity NPC88325
0.6471 Remote Similarity NPC470893
0.6471 Remote Similarity NPC223604
0.6471 Remote Similarity NPC469770
0.6458 Remote Similarity NPC32351
0.641 Remote Similarity NPC62779
0.64 Remote Similarity NPC476679
0.6389 Remote Similarity NPC64176
0.6389 Remote Similarity NPC288991
0.6389 Remote Similarity NPC262789
0.6383 Remote Similarity NPC91962
0.6383 Remote Similarity NPC178644
0.6364 Remote Similarity NPC105246
0.6364 Remote Similarity NPC190232
0.6346 Remote Similarity NPC96663
0.6327 Remote Similarity NPC27438
0.6327 Remote Similarity NPC26906
0.6327 Remote Similarity NPC214584
0.6327 Remote Similarity NPC244038
0.6316 Remote Similarity NPC196831
0.6286 Remote Similarity NPC287191
0.6286 Remote Similarity NPC266144
0.6286 Remote Similarity NPC31891
0.6286 Remote Similarity NPC266539
0.6279 Remote Similarity NPC78551
0.6279 Remote Similarity NPC62086
0.6279 Remote Similarity NPC227632
0.6279 Remote Similarity NPC246165
0.625 Remote Similarity NPC234597
0.6226 Remote Similarity NPC11130
0.6226 Remote Similarity NPC230823
0.6222 Remote Similarity NPC106819
0.6222 Remote Similarity NPC192529
0.62 Remote Similarity NPC177112
0.62 Remote Similarity NPC68014
0.62 Remote Similarity NPC473728
0.62 Remote Similarity NPC179169
0.62 Remote Similarity NPC181255
0.62 Remote Similarity NPC35519
0.62 Remote Similarity NPC294358
0.62 Remote Similarity NPC71506
0.62 Remote Similarity NPC157781
0.62 Remote Similarity NPC306195
0.62 Remote Similarity NPC40417
0.619 Remote Similarity NPC180840
0.6154 Remote Similarity NPC13217
0.6154 Remote Similarity NPC123194
0.6154 Remote Similarity NPC329686
0.6136 Remote Similarity NPC473614
0.6136 Remote Similarity NPC103290
0.6136 Remote Similarity NPC269823
0.6136 Remote Similarity NPC469969
0.6122 Remote Similarity NPC176819
0.6122 Remote Similarity NPC289388
0.6122 Remote Similarity NPC163984
0.6122 Remote Similarity NPC58970
0.6122 Remote Similarity NPC200129
0.6111 Remote Similarity NPC226848
0.6111 Remote Similarity NPC469769
0.6111 Remote Similarity NPC181872
0.6078 Remote Similarity NPC14002
0.6078 Remote Similarity NPC268564
0.6078 Remote Similarity NPC23117
0.6038 Remote Similarity NPC473865
0.6038 Remote Similarity NPC474643
0.6038 Remote Similarity NPC473733
0.6 Remote Similarity NPC51758
0.6 Remote Similarity NPC209279
0.6 Remote Similarity NPC193180
0.6 Remote Similarity NPC68889
0.6 Remote Similarity NPC172053
0.6 Remote Similarity NPC5698
0.6 Remote Similarity NPC180871
0.6 Remote Similarity NPC244452
0.6 Remote Similarity NPC475931
0.6 Remote Similarity NPC194586
0.6 Remote Similarity NPC122239
0.6 Remote Similarity NPC108494
0.6 Remote Similarity NPC38513
0.6 Remote Similarity NPC88079
0.6 Remote Similarity NPC213538
0.6 Remote Similarity NPC256766
0.6 Remote Similarity NPC67761
0.5962 Remote Similarity NPC63396
0.5962 Remote Similarity NPC5626
0.5962 Remote Similarity NPC202850
0.5952 Remote Similarity NPC185839
0.5926 Remote Similarity NPC55004
0.5926 Remote Similarity NPC474528
0.5926 Remote Similarity NPC267626
0.5926 Remote Similarity NPC474415
0.5926 Remote Similarity NPC474457
0.5926 Remote Similarity NPC475696
0.5926 Remote Similarity NPC49575
0.5918 Remote Similarity NPC62755
0.5893 Remote Similarity NPC323153
0.5893 Remote Similarity NPC252809
0.5893 Remote Similarity NPC471081
0.5893 Remote Similarity NPC176621
0.5882 Remote Similarity NPC216407
0.5882 Remote Similarity NPC170167
0.587 Remote Similarity NPC166362
0.587 Remote Similarity NPC474118
0.587 Remote Similarity NPC301972
0.587 Remote Similarity NPC141777
0.587 Remote Similarity NPC227670
0.587 Remote Similarity NPC90803
0.587 Remote Similarity NPC90506
0.587 Remote Similarity NPC116934
0.587 Remote Similarity NPC23145
0.587 Remote Similarity NPC51762
0.5849 Remote Similarity NPC232247
0.5849 Remote Similarity NPC130209
0.5849 Remote Similarity NPC281590
0.5849 Remote Similarity NPC148163
0.5849 Remote Similarity NPC188789
0.5849 Remote Similarity NPC474644
0.5849 Remote Similarity NPC251666
0.5849 Remote Similarity NPC477984
0.5849 Remote Similarity NPC275472
0.5849 Remote Similarity NPC148216
0.5833 Remote Similarity NPC236355
0.5833 Remote Similarity NPC4079
0.5833 Remote Similarity NPC14917
0.5833 Remote Similarity NPC159420
0.5818 Remote Similarity NPC472830
0.5818 Remote Similarity NPC60772
0.5818 Remote Similarity NPC266295
0.5818 Remote Similarity NPC30215
0.5818 Remote Similarity NPC94991
0.58 Remote Similarity NPC474460
0.5789 Remote Similarity NPC210346
0.5789 Remote Similarity NPC60565

  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 NPC92224 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
0.8611 High Similarity NPD319 Phase 1
0.6957 Remote Similarity NPD8262 Approved
0.6429 Remote Similarity NPD5783 Phase 3
0.6364 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5849 Remote Similarity NPD342 Phase 1
0.5741 Remote Similarity NPD4219 Approved
0.5625 Remote Similarity NPD4265 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