Structure

Physi-Chem Properties

Molecular Weight:  220.18
Volume:  260.321
LogP:  3.603
LogD:  3.484
LogS:  -4.381
# Rotatable Bonds:  1
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.602
Synthetic Accessibility Score:  3.775
Fsp3:  0.667
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:  -4.526
MDCK Permeability:  2.3350472474703565e-05
Pgp-inhibitor:  0.157
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.216
30% Bioavailability (F30%):  0.344

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.678
Plasma Protein Binding (PPB):  96.72228240966797%
Volume Distribution (VD):  1.052
Pgp-substrate:  1.4471971988677979%

ADMET: Metabolism

CYP1A2-inhibitor:  0.356
CYP1A2-substrate:  0.739
CYP2C19-inhibitor:  0.519
CYP2C19-substrate:  0.927
CYP2C9-inhibitor:  0.624
CYP2C9-substrate:  0.931
CYP2D6-inhibitor:  0.098
CYP2D6-substrate:  0.643
CYP3A4-inhibitor:  0.295
CYP3A4-substrate:  0.526

ADMET: Excretion

Clearance (CL):  3.024
Half-life (T1/2):  0.542

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.16
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.15
Skin Sensitization:  0.939
Carcinogencity:  0.073
Eye Corrosion:  0.739
Eye Irritation:  0.969
Respiratory Toxicity:  0.45

Download Data

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

  Natural Product: NPC27438

Natural Product ID:  NPC27438
Common Name*:   (+)-Preisocalamenediol
IUPAC Name:   (2S,5E)-5-methyl-9-methylidene-2-propan-2-ylcyclodec-5-en-1-one
Synonyms:   (+)-Preisocalamenediol
Standard InCHIKey:  QTFJNWQFKJITEE-CYIWUNGXSA-N
Standard InCHI:  InChI=1S/C15H24O/c1-11(2)14-9-8-12(3)6-5-7-13(4)10-15(14)16/h6,10-11,14H,5,7-9H2,1-4H3/b12-6+,13-10+/t14-/m0/s1
SMILES:  CC(C)[C@@H]1CC/C(=C/CC/C(=C/C1=O)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1814553
PubChem CID:   12305706
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
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[21563811]
NPO25682 Acorus calamus Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[22671987]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[23373216]
NPO96 Rhododendron capitatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21996 Baccharis latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29031 Rhizoma acori graminei n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO96 Rhododendron capitatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO96 Rhododendron capitatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO96 Rhododendron capitatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21996 Baccharis latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25682 Acorus calamus Species Acoraceae 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
NPT2 Others Unspecified Emax = 886.0 % PMID[483039]
NPT2 Others Unspecified EC50 = 135100.0 nM PMID[483039]

☑ 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 NPC27438 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
0.94 High Similarity NPC63396
0.94 High Similarity NPC202850
0.8846 High Similarity NPC275472
0.8462 Intermediate Similarity NPC268564
0.8235 Intermediate Similarity NPC32351
0.82 Intermediate Similarity NPC91962
0.8182 Intermediate Similarity NPC49575
0.8182 Intermediate Similarity NPC55004
0.8182 Intermediate Similarity NPC267626
0.8182 Intermediate Similarity NPC230823
0.8182 Intermediate Similarity NPC193695
0.8113 Intermediate Similarity NPC474141
0.8036 Intermediate Similarity NPC94991
0.8036 Intermediate Similarity NPC30215
0.8036 Intermediate Similarity NPC266295
0.8 Intermediate Similarity NPC20603
0.7895 Intermediate Similarity NPC143834
0.7895 Intermediate Similarity NPC259261
0.7895 Intermediate Similarity NPC285594
0.7895 Intermediate Similarity NPC472304
0.7895 Intermediate Similarity NPC96551
0.7895 Intermediate Similarity NPC276764
0.7857 Intermediate Similarity NPC115385
0.7778 Intermediate Similarity NPC45283
0.7759 Intermediate Similarity NPC25853
0.7759 Intermediate Similarity NPC127582
0.7755 Intermediate Similarity NPC301972
0.7736 Intermediate Similarity NPC236623
0.7705 Intermediate Similarity NPC197089
0.7679 Intermediate Similarity NPC473733
0.7647 Intermediate Similarity NPC8610
0.7647 Intermediate Similarity NPC14917
0.7647 Intermediate Similarity NPC262558
0.7647 Intermediate Similarity NPC236355
0.7647 Intermediate Similarity NPC22098
0.7647 Intermediate Similarity NPC4079
0.7647 Intermediate Similarity NPC276009
0.7647 Intermediate Similarity NPC195246
0.7627 Intermediate Similarity NPC60565
0.7627 Intermediate Similarity NPC213152
0.7627 Intermediate Similarity NPC475795
0.7593 Intermediate Similarity NPC471751
0.7547 Intermediate Similarity NPC163984
0.7547 Intermediate Similarity NPC58970
0.7547 Intermediate Similarity NPC176819
0.7547 Intermediate Similarity NPC116906
0.75 Intermediate Similarity NPC200258
0.75 Intermediate Similarity NPC165695
0.75 Intermediate Similarity NPC197238
0.75 Intermediate Similarity NPC202118
0.7455 Intermediate Similarity NPC296311
0.7414 Intermediate Similarity NPC56905
0.7414 Intermediate Similarity NPC308108
0.7414 Intermediate Similarity NPC27610
0.7414 Intermediate Similarity NPC311852
0.7414 Intermediate Similarity NPC170799
0.7407 Intermediate Similarity NPC64866
0.7377 Intermediate Similarity NPC212210
0.7377 Intermediate Similarity NPC469662
0.7377 Intermediate Similarity NPC6697
0.7377 Intermediate Similarity NPC285371
0.7377 Intermediate Similarity NPC475124
0.7377 Intermediate Similarity NPC473902
0.7358 Intermediate Similarity NPC145311
0.7333 Intermediate Similarity NPC97322
0.7308 Intermediate Similarity NPC100380
0.7258 Intermediate Similarity NPC251118
0.7255 Intermediate Similarity NPC25771
0.7241 Intermediate Similarity NPC192427
0.7234 Intermediate Similarity NPC185839
0.7213 Intermediate Similarity NPC32285
0.7213 Intermediate Similarity NPC167256
0.7213 Intermediate Similarity NPC288253
0.7143 Intermediate Similarity NPC23117
0.7097 Intermediate Similarity NPC150162
0.7083 Intermediate Similarity NPC92863
0.7083 Intermediate Similarity NPC155880
0.7083 Intermediate Similarity NPC180840
0.7059 Intermediate Similarity NPC292463
0.7059 Intermediate Similarity NPC86538
0.7059 Intermediate Similarity NPC106819
0.7031 Intermediate Similarity NPC475523
0.7021 Intermediate Similarity NPC38497
0.7018 Intermediate Similarity NPC95581
0.7015 Intermediate Similarity NPC275098
0.7 Intermediate Similarity NPC218918
0.7 Intermediate Similarity NPC120926
0.6984 Remote Similarity NPC470329
0.6964 Remote Similarity NPC216407
0.6964 Remote Similarity NPC68014
0.6923 Remote Similarity NPC469688
0.6923 Remote Similarity NPC20610
0.6923 Remote Similarity NPC39157
0.6923 Remote Similarity NPC296697
0.6923 Remote Similarity NPC155198
0.6923 Remote Similarity NPC310992
0.6923 Remote Similarity NPC82477
0.6923 Remote Similarity NPC260474
0.6923 Remote Similarity NPC87141
0.6923 Remote Similarity NPC188292
0.6923 Remote Similarity NPC142754
0.6909 Remote Similarity NPC15325
0.6909 Remote Similarity NPC228776
0.6897 Remote Similarity NPC188789
0.6897 Remote Similarity NPC477984
0.6875 Remote Similarity NPC323005
0.6842 Remote Similarity NPC37644
0.6842 Remote Similarity NPC14002
0.6833 Remote Similarity NPC60772
0.6825 Remote Similarity NPC4638
0.6818 Remote Similarity NPC286814
0.6818 Remote Similarity NPC182815
0.6818 Remote Similarity NPC296522
0.6818 Remote Similarity NPC61702
0.6818 Remote Similarity NPC144511
0.6818 Remote Similarity NPC162867
0.6818 Remote Similarity NPC139397
0.6818 Remote Similarity NPC469677
0.6818 Remote Similarity NPC256846
0.6792 Remote Similarity NPC166788
0.6769 Remote Similarity NPC278895
0.6769 Remote Similarity NPC220210
0.6769 Remote Similarity NPC20181
0.6724 Remote Similarity NPC209431
0.6724 Remote Similarity NPC5626
0.6724 Remote Similarity NPC100809
0.6719 Remote Similarity NPC474329
0.6719 Remote Similarity NPC474304
0.6719 Remote Similarity NPC268039
0.6716 Remote Similarity NPC282593
0.6716 Remote Similarity NPC477856
0.6716 Remote Similarity NPC2634
0.6716 Remote Similarity NPC35734
0.6716 Remote Similarity NPC251929
0.6716 Remote Similarity NPC159577
0.6716 Remote Similarity NPC265782
0.6716 Remote Similarity NPC260040
0.6716 Remote Similarity NPC307176
0.6716 Remote Similarity NPC214770
0.6667 Remote Similarity NPC22182
0.6667 Remote Similarity NPC157781
0.6667 Remote Similarity NPC35519
0.6667 Remote Similarity NPC472306
0.6667 Remote Similarity NPC306195
0.6667 Remote Similarity NPC181255
0.6667 Remote Similarity NPC469679
0.6667 Remote Similarity NPC179169
0.6667 Remote Similarity NPC165808
0.6667 Remote Similarity NPC471752
0.6667 Remote Similarity NPC476614
0.6618 Remote Similarity NPC54123
0.6618 Remote Similarity NPC133253
0.6618 Remote Similarity NPC21944
0.6618 Remote Similarity NPC190035
0.6618 Remote Similarity NPC470078
0.6618 Remote Similarity NPC181204
0.6618 Remote Similarity NPC115023
0.6618 Remote Similarity NPC474562
0.6618 Remote Similarity NPC129665
0.6615 Remote Similarity NPC304665
0.6615 Remote Similarity NPC126899
0.6615 Remote Similarity NPC154728
0.6613 Remote Similarity NPC40206
0.6607 Remote Similarity NPC329773
0.6571 Remote Similarity NPC155587
0.6567 Remote Similarity NPC469914
0.6567 Remote Similarity NPC477449
0.6567 Remote Similarity NPC474060
0.6567 Remote Similarity NPC477448
0.6562 Remote Similarity NPC234767
0.6557 Remote Similarity NPC329819
0.6552 Remote Similarity NPC69898
0.6552 Remote Similarity NPC295777
0.6538 Remote Similarity NPC177470
0.6538 Remote Similarity NPC473912
0.6522 Remote Similarity NPC107783
0.6522 Remote Similarity NPC92909
0.6522 Remote Similarity NPC470237
0.6522 Remote Similarity NPC56747
0.6522 Remote Similarity NPC180015
0.6522 Remote Similarity NPC474228
0.6522 Remote Similarity NPC470045
0.6522 Remote Similarity NPC474488
0.6522 Remote Similarity NPC303613
0.6522 Remote Similarity NPC251705
0.6522 Remote Similarity NPC130016
0.6522 Remote Similarity NPC109576
0.6522 Remote Similarity NPC470044
0.6522 Remote Similarity NPC300940
0.6515 Remote Similarity NPC193770
0.6515 Remote Similarity NPC290350
0.6515 Remote Similarity NPC4370
0.6515 Remote Similarity NPC60120
0.6508 Remote Similarity NPC260573
0.6508 Remote Similarity NPC64985
0.65 Remote Similarity NPC141699
0.6491 Remote Similarity NPC477458
0.6491 Remote Similarity NPC214584
0.6491 Remote Similarity NPC234829
0.6491 Remote Similarity NPC26906

  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 NPC27438 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
0.7414 Intermediate Similarity NPD287 Approved
0.6939 Remote Similarity NPD5783 Phase 3
0.6923 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6818 Remote Similarity NPD4137 Phase 3
0.6716 Remote Similarity NPD4747 Approved
0.6716 Remote Similarity NPD4691 Approved
0.6618 Remote Similarity NPD5276 Approved
0.6615 Remote Similarity NPD7331 Phase 2
0.6429 Remote Similarity NPD5733 Approved
0.6429 Remote Similarity NPD4058 Approved
0.6429 Remote Similarity NPD4687 Approved
0.6212 Remote Similarity NPD7341 Phase 2
0.62 Remote Similarity NPD319 Phase 1
0.5932 Remote Similarity NPD28 Approved
0.5932 Remote Similarity NPD29 Approved
0.5921 Remote Similarity NPD4695 Discontinued
0.5893 Remote Similarity NPD3174 Discontinued
0.5867 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5806 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5789 Remote Similarity NPD345 Approved
0.5789 Remote Similarity NPD344 Approved
0.5789 Remote Similarity NPD343 Approved
0.5769 Remote Similarity NPD4221 Approved
0.5769 Remote Similarity NPD3667 Approved
0.5769 Remote Similarity NPD4223 Phase 3
0.5738 Remote Similarity NPD3172 Approved
0.5714 Remote Similarity NPD5368 Approved
0.5696 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5672 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5652 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5645 Remote Similarity NPD3194 Approved
0.5645 Remote Similarity NPD3196 Approved
0.5645 Remote Similarity NPD4266 Approved
0.5645 Remote Similarity NPD3195 Phase 2
0.5641 Remote Similarity NPD5369 Approved
0.5641 Remote Similarity NPD8028 Phase 2
0.5636 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3668 Phase 3
0.5625 Remote Similarity NPD4786 Approved
0.5625 Remote Similarity NPD4197 Approved
0.5625 Remote Similarity NPD3666 Approved
0.5625 Remote Similarity NPD3665 Phase 1
0.5625 Remote Similarity NPD3133 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