Structure

Physi-Chem Properties

Molecular Weight:  256.18
Volume:  304.299
LogP:  5.395
LogD:  4.385
LogS:  -5.194
# Rotatable Bonds:  5
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.407
Synthetic Accessibility Score:  3.899
Fsp3:  0.611
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:  -4.254
MDCK Permeability:  2.5318200641777366e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.031
30% Bioavailability (F30%):  0.068

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.026
Plasma Protein Binding (PPB):  100.5844955444336%
Volume Distribution (VD):  1.481
Pgp-substrate:  1.4223120212554932%

ADMET: Metabolism

CYP1A2-inhibitor:  0.866
CYP1A2-substrate:  0.606
CYP2C19-inhibitor:  0.902
CYP2C19-substrate:  0.554
CYP2C9-inhibitor:  0.886
CYP2C9-substrate:  0.978
CYP2D6-inhibitor:  0.031
CYP2D6-substrate:  0.184
CYP3A4-inhibitor:  0.812
CYP3A4-substrate:  0.162

ADMET: Excretion

Clearance (CL):  8.075
Half-life (T1/2):  0.16

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.939
Drug-inuced Liver Injury (DILI):  0.966
AMES Toxicity:  0.776
Rat Oral Acute Toxicity:  0.323
Maximum Recommended Daily Dose:  0.765
Skin Sensitization:  0.932
Carcinogencity:  0.324
Eye Corrosion:  0.903
Eye Irritation:  0.975
Respiratory Toxicity:  0.961

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

  Natural Product: NPC473733

Natural Product ID:  NPC473733
Common Name*:   Montiporyine F
IUPAC Name:   3-methyl-5-undeca-1,3-diynylcyclohex-2-en-1-one
Synonyms:   montiporyine F
Standard InCHIKey:  IQGBPJFXIUKNHN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H24O/c1-3-4-5-6-7-8-9-10-11-12-17-13-16(2)14-18(19)15-17/h14,17H,3-8,13,15H2,1-2H3
SMILES:  CCCCCCCC#CC#CC1CC(=CC(=O)C1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450527
PubChem CID:   10801096
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0004325] Cyclohexenones

*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
NPO33414 montipora sp. Species Acroporidae Eukaryota n.a. n.a. n.a. PMID[11087594]
NPO33414 montipora sp. Species Acroporidae Eukaryota n.a. n.a. n.a. PMID[11520227]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 > 50.0 ug ml-1 PMID[541860]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 29.2 ug ml-1 PMID[541860]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 36.7 ug ml-1 PMID[541860]
NPT574 Cell Line XF498 Homo sapiens ED50 = 31.3 ug ml-1 PMID[541860]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 45.1 ug ml-1 PMID[541860]

☑ 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 NPC473733 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
0.8846 High Similarity NPC32351
0.8364 Intermediate Similarity NPC268564
0.8333 Intermediate Similarity NPC64866
0.8148 Intermediate Similarity NPC58970
0.8148 Intermediate Similarity NPC176819
0.8148 Intermediate Similarity NPC163984
0.8136 Intermediate Similarity NPC472304
0.8136 Intermediate Similarity NPC276764
0.8113 Intermediate Similarity NPC91962
0.8 Intermediate Similarity NPC127582
0.7966 Intermediate Similarity NPC311852
0.7925 Intermediate Similarity NPC14917
0.7925 Intermediate Similarity NPC262558
0.7925 Intermediate Similarity NPC236355
0.7925 Intermediate Similarity NPC4079
0.7925 Intermediate Similarity NPC8610
0.7885 Intermediate Similarity NPC25771
0.7869 Intermediate Similarity NPC213152
0.7778 Intermediate Similarity NPC251118
0.7759 Intermediate Similarity NPC275472
0.7719 Intermediate Similarity NPC474141
0.7719 Intermediate Similarity NPC23117
0.7692 Intermediate Similarity NPC292463
0.7679 Intermediate Similarity NPC27438
0.7667 Intermediate Similarity NPC94991
0.7667 Intermediate Similarity NPC308108
0.7667 Intermediate Similarity NPC266295
0.7667 Intermediate Similarity NPC56905
0.7667 Intermediate Similarity NPC27610
0.7667 Intermediate Similarity NPC170799
0.7619 Intermediate Similarity NPC212210
0.7619 Intermediate Similarity NPC6697
0.7619 Intermediate Similarity NPC475124
0.7619 Intermediate Similarity NPC285371
0.7541 Intermediate Similarity NPC259261
0.75 Intermediate Similarity NPC115385
0.75 Intermediate Similarity NPC193695
0.75 Intermediate Similarity NPC474391
0.746 Intermediate Similarity NPC197238
0.746 Intermediate Similarity NPC288253
0.746 Intermediate Similarity NPC165695
0.746 Intermediate Similarity NPC202118
0.7424 Intermediate Similarity NPC155198
0.7424 Intermediate Similarity NPC188292
0.7424 Intermediate Similarity NPC87141
0.7424 Intermediate Similarity NPC310992
0.7424 Intermediate Similarity NPC260474
0.7419 Intermediate Similarity NPC25853
0.7414 Intermediate Similarity NPC37644
0.7414 Intermediate Similarity NPC45283
0.7414 Intermediate Similarity NPC14002
0.7407 Intermediate Similarity NPC166788
0.7407 Intermediate Similarity NPC191337
0.7377 Intermediate Similarity NPC30215
0.7344 Intermediate Similarity NPC4638
0.7344 Intermediate Similarity NPC150162
0.7344 Intermediate Similarity NPC469662
0.7333 Intermediate Similarity NPC20603
0.7321 Intermediate Similarity NPC145311
0.7313 Intermediate Similarity NPC139397
0.7313 Intermediate Similarity NPC256846
0.7302 Intermediate Similarity NPC97322
0.7302 Intermediate Similarity NPC60565
0.7288 Intermediate Similarity NPC209431
0.7288 Intermediate Similarity NPC63396
0.7288 Intermediate Similarity NPC100809
0.7288 Intermediate Similarity NPC202850
0.7288 Intermediate Similarity NPC5626
0.7273 Intermediate Similarity NPC100380
0.7273 Intermediate Similarity NPC475523
0.7258 Intermediate Similarity NPC96551
0.7258 Intermediate Similarity NPC143834
0.7258 Intermediate Similarity NPC285594
0.7241 Intermediate Similarity NPC471751
0.7231 Intermediate Similarity NPC470329
0.7222 Intermediate Similarity NPC145755
0.7222 Intermediate Similarity NPC477686
0.7222 Intermediate Similarity NPC267514
0.7213 Intermediate Similarity NPC230823
0.7213 Intermediate Similarity NPC267626
0.7213 Intermediate Similarity NPC49575
0.7213 Intermediate Similarity NPC55004
0.7206 Intermediate Similarity NPC251929
0.7206 Intermediate Similarity NPC307176
0.7206 Intermediate Similarity NPC260040
0.7206 Intermediate Similarity NPC265782
0.7206 Intermediate Similarity NPC159577
0.7206 Intermediate Similarity NPC2634
0.7206 Intermediate Similarity NPC282593
0.7206 Intermediate Similarity NPC35734
0.7193 Intermediate Similarity NPC15325
0.7193 Intermediate Similarity NPC228776
0.7193 Intermediate Similarity NPC118788
0.7193 Intermediate Similarity NPC116906
0.7188 Intermediate Similarity NPC32285
0.7167 Intermediate Similarity NPC477984
0.7119 Intermediate Similarity NPC296311
0.7101 Intermediate Similarity NPC190035
0.7101 Intermediate Similarity NPC115023
0.7101 Intermediate Similarity NPC54123
0.7097 Intermediate Similarity NPC60772
0.7077 Intermediate Similarity NPC473902
0.7059 Intermediate Similarity NPC469914
0.7059 Intermediate Similarity NPC474060
0.7037 Intermediate Similarity NPC301972
0.7031 Intermediate Similarity NPC475795
0.7 Intermediate Similarity NPC303613
0.7 Intermediate Similarity NPC109576
0.7 Intermediate Similarity NPC470044
0.7 Intermediate Similarity NPC474228
0.7 Intermediate Similarity NPC470045
0.7 Intermediate Similarity NPC130016
0.7 Intermediate Similarity NPC180015
0.7 Intermediate Similarity NPC56747
0.7 Intermediate Similarity NPC251705
0.6964 Remote Similarity NPC22098
0.6964 Remote Similarity NPC195246
0.6964 Remote Similarity NPC276009
0.6957 Remote Similarity NPC151045
0.6957 Remote Similarity NPC246722
0.6935 Remote Similarity NPC192427
0.6923 Remote Similarity NPC167256
0.6912 Remote Similarity NPC82477
0.6912 Remote Similarity NPC142754
0.6912 Remote Similarity NPC20610
0.6912 Remote Similarity NPC296697
0.6912 Remote Similarity NPC39157
0.6901 Remote Similarity NPC309852
0.6885 Remote Similarity NPC200258
0.6885 Remote Similarity NPC188789
0.6866 Remote Similarity NPC323005
0.6857 Remote Similarity NPC133253
0.6857 Remote Similarity NPC474562
0.6857 Remote Similarity NPC225467
0.6857 Remote Similarity NPC234707
0.6857 Remote Similarity NPC5701
0.6857 Remote Similarity NPC181204
0.6833 Remote Similarity NPC295777
0.6833 Remote Similarity NPC69898
0.6825 Remote Similarity NPC329819
0.6812 Remote Similarity NPC182815
0.6812 Remote Similarity NPC286814
0.6806 Remote Similarity NPC473171
0.6806 Remote Similarity NPC293803
0.6806 Remote Similarity NPC65650
0.6806 Remote Similarity NPC476346
0.678 Remote Similarity NPC234829
0.678 Remote Similarity NPC236623
0.678 Remote Similarity NPC477458
0.6765 Remote Similarity NPC290350
0.6765 Remote Similarity NPC220210
0.6765 Remote Similarity NPC4370
0.6765 Remote Similarity NPC20181
0.6761 Remote Similarity NPC276336
0.6731 Remote Similarity NPC180840
0.6721 Remote Similarity NPC250539
0.6716 Remote Similarity NPC61473
0.6712 Remote Similarity NPC69408
0.6712 Remote Similarity NPC110725
0.6712 Remote Similarity NPC1254
0.6712 Remote Similarity NPC180886
0.6667 Remote Similarity NPC474796
0.6667 Remote Similarity NPC255021
0.6667 Remote Similarity NPC7754
0.6667 Remote Similarity NPC469688
0.6667 Remote Similarity NPC472306
0.6667 Remote Similarity NPC20025
0.6667 Remote Similarity NPC474797
0.6667 Remote Similarity NPC477707
0.6667 Remote Similarity NPC329866
0.6667 Remote Similarity NPC471752
0.6667 Remote Similarity NPC270170
0.6667 Remote Similarity NPC477830
0.6622 Remote Similarity NPC165711
0.6622 Remote Similarity NPC472300
0.662 Remote Similarity NPC474539
0.662 Remote Similarity NPC470078
0.662 Remote Similarity NPC305501
0.662 Remote Similarity NPC21944
0.6618 Remote Similarity NPC92327
0.6618 Remote Similarity NPC176171
0.6575 Remote Similarity NPC114236
0.6571 Remote Similarity NPC136473
0.6571 Remote Similarity NPC477448
0.6571 Remote Similarity NPC477449
0.6567 Remote Similarity NPC52449
0.6567 Remote Similarity NPC169275
0.6567 Remote Similarity NPC474400
0.6567 Remote Similarity NPC34622
0.6552 Remote Similarity NPC471958
0.6538 Remote Similarity NPC185839
0.6533 Remote Similarity NPC475994
0.6533 Remote Similarity NPC189485
0.6533 Remote Similarity NPC478246
0.6533 Remote Similarity NPC478247
0.6533 Remote Similarity NPC275494
0.6533 Remote Similarity NPC115515
0.6533 Remote Similarity NPC74410
0.6533 Remote Similarity NPC471409
0.6528 Remote Similarity NPC186042

  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 NPC473733 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
0.7667 Intermediate Similarity NPD287 Approved
0.7458 Intermediate Similarity NPD4627 Clinical (unspecified phase)
0.7313 Intermediate Similarity NPD4137 Phase 3
0.7206 Intermediate Similarity NPD4747 Approved
0.7206 Intermediate Similarity NPD4691 Approved
0.7121 Intermediate Similarity NPD7331 Phase 2
0.7101 Intermediate Similarity NPD5276 Approved
0.6912 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6901 Remote Similarity NPD4687 Approved
0.6901 Remote Similarity NPD5733 Approved
0.6901 Remote Similarity NPD4058 Approved
0.6716 Remote Similarity NPD7341 Phase 2
0.6604 Remote Similarity NPD5783 Phase 3
0.65 Remote Similarity NPD4519 Discontinued
0.65 Remote Similarity NPD4138 Approved
0.65 Remote Similarity NPD4623 Approved
0.65 Remote Similarity NPD4688 Approved
0.65 Remote Similarity NPD4690 Approved
0.65 Remote Similarity NPD4689 Approved
0.65 Remote Similarity NPD5205 Approved
0.65 Remote Similarity NPD4693 Phase 3
0.6418 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6377 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6364 Remote Similarity NPD4695 Discontinued
0.6341 Remote Similarity NPD5208 Approved
0.6226 Remote Similarity NPD319 Phase 1
0.6203 Remote Similarity NPD4221 Approved
0.6203 Remote Similarity NPD4223 Phase 3
0.6145 Remote Similarity NPD4518 Approved
0.6125 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6076 Remote Similarity NPD8028 Phase 2
0.6049 Remote Similarity NPD3666 Approved
0.6049 Remote Similarity NPD3665 Phase 1
0.6049 Remote Similarity NPD3133 Approved
0.6049 Remote Similarity NPD4197 Approved
0.6029 Remote Similarity NPD4194 Approved
0.6029 Remote Similarity NPD4191 Approved
0.6029 Remote Similarity NPD4192 Approved
0.6029 Remote Similarity NPD4193 Approved
0.5976 Remote Similarity NPD5329 Approved
0.5949 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5909 Remote Similarity NPD8779 Phase 3
0.5904 Remote Similarity NPD3618 Phase 1
0.5904 Remote Similarity NPD7334 Approved
0.5904 Remote Similarity NPD7521 Approved
0.5904 Remote Similarity NPD6684 Approved
0.5904 Remote Similarity NPD5280 Approved
0.5904 Remote Similarity NPD5330 Approved
0.5904 Remote Similarity NPD6409 Approved
0.5904 Remote Similarity NPD5279 Phase 3
0.5904 Remote Similarity NPD4694 Approved
0.5904 Remote Similarity NPD5690 Phase 2
0.5904 Remote Similarity NPD7146 Approved
0.5897 Remote Similarity NPD3617 Approved
0.5875 Remote Similarity NPD4692 Approved
0.5875 Remote Similarity NPD4139 Approved
0.5833 Remote Similarity NPD3573 Approved
0.5802 Remote Similarity NPD3667 Approved
0.5765 Remote Similarity NPD5737 Approved
0.5765 Remote Similarity NPD6672 Approved
0.5765 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5765 Remote Similarity NPD6903 Approved
0.5714 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5714 Remote Similarity NPD29 Approved
0.5714 Remote Similarity NPD28 Approved
0.5698 Remote Similarity NPD4753 Phase 2
0.5698 Remote Similarity NPD6904 Approved
0.5698 Remote Similarity NPD5328 Approved
0.5698 Remote Similarity NPD6080 Approved
0.5698 Remote Similarity NPD6673 Approved
0.5694 Remote Similarity NPD3704 Approved
0.5667 Remote Similarity NPD3174 Discontinued
0.5663 Remote Similarity NPD4786 Approved
0.5663 Remote Similarity NPD3668 Phase 3
0.5632 Remote Similarity NPD4096 Approved
0.5632 Remote Similarity NPD5692 Phase 3
0.5632 Remote Similarity NPD5207 Approved
0.5625 Remote Similarity NPD4195 Approved
0.5616 Remote Similarity NPD3709 Clinical (unspecified phase)
0.561 Remote Similarity NPD4752 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