Structure

Physi-Chem Properties

Molecular Weight:  339.24
Volume:  372.792
LogP:  4.133
LogD:  2.612
LogS:  -2.895
# Rotatable Bonds:  15
TPSA:  87.45
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.204
Synthetic Accessibility Score:  3.458
Fsp3:  0.737
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.381
MDCK Permeability:  0.0001181957995868288
Pgp-inhibitor:  0.021
Pgp-substrate:  0.053
Human Intestinal Absorption (HIA):  0.49
20% Bioavailability (F20%):  0.911
30% Bioavailability (F30%):  0.536

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.772
Plasma Protein Binding (PPB):  80.74563598632812%
Volume Distribution (VD):  0.612
Pgp-substrate:  12.468602180480957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.053
CYP1A2-substrate:  0.115
CYP2C19-inhibitor:  0.071
CYP2C19-substrate:  0.33
CYP2C9-inhibitor:  0.398
CYP2C9-substrate:  0.981
CYP2D6-inhibitor:  0.064
CYP2D6-substrate:  0.226
CYP3A4-inhibitor:  0.044
CYP3A4-substrate:  0.063

ADMET: Excretion

Clearance (CL):  2.757
Half-life (T1/2):  0.828

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.894
Drug-inuced Liver Injury (DILI):  0.96
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.064
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.931
Carcinogencity:  0.208
Eye Corrosion:  0.996
Eye Irritation:  0.982
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC477487

Natural Product ID:  NPC477487
Common Name*:   2-[(E)-5-methyl-3-oxododec-4-enimidoyl]oxyhexanoic acid
IUPAC Name:   2-[(E)-5-methyl-3-oxododec-4-enimidoyl]oxyhexanoic acid
Synonyms:  
Standard InCHIKey:  KBHGLYOHUPGXNX-KPQNYSBDSA-N
Standard InCHI:  InChI=1S/C19H33NO4/c1-4-6-8-9-10-11-15(3)13-16(21)14-18(20)24-17(19(22)23)12-7-5-2/h13,17,20H,4-12,14H2,1-3H3,(H,22,23)/b15-13+,20-18?
SMILES:  CCCCCCC/C(=C/C(=O)CC(=N)OC(CCCC)C(=O)O)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   23642822
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-chain fatty acids

*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
NPO33549 Marinispora sp. NPS008920 Species n.a. n.a. n.a. Cocos Lagoon, Guam 2002-JAN PMID[17845000]

☑ 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
NPT19 Organism Escherichia coli Escherichia coli MIC > 32 ug/ml PMID[17845000]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 32 ug/ml PMID[17845000]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC > 32 ug/ml PMID[17845000]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 24 ug/ml PMID[17845000]
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC > 32 ug/ml PMID[17845000]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 32 ug/ml PMID[17845000]

☑ 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 NPC477487 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
0.7407 Intermediate Similarity NPC42526
0.7143 Intermediate Similarity NPC472009
0.7143 Intermediate Similarity NPC474321
0.7143 Intermediate Similarity NPC160540
0.7065 Intermediate Similarity NPC472007
0.7037 Intermediate Similarity NPC22101
0.7037 Intermediate Similarity NPC127091
0.7037 Intermediate Similarity NPC271921
0.7037 Intermediate Similarity NPC148192
0.7037 Intermediate Similarity NPC104537
0.7037 Intermediate Similarity NPC330426
0.6989 Remote Similarity NPC472008
0.6977 Remote Similarity NPC205615
0.6977 Remote Similarity NPC16279
0.6977 Remote Similarity NPC256640
0.6961 Remote Similarity NPC271269
0.6951 Remote Similarity NPC141481
0.6951 Remote Similarity NPC473559
0.6951 Remote Similarity NPC324981
0.6951 Remote Similarity NPC48218
0.6932 Remote Similarity NPC471740
0.6914 Remote Similarity NPC83965
0.6882 Remote Similarity NPC471738
0.6869 Remote Similarity NPC313440
0.6854 Remote Similarity NPC472948
0.6854 Remote Similarity NPC47653
0.6829 Remote Similarity NPC473829
0.6829 Remote Similarity NPC475443
0.6813 Remote Similarity NPC144415
0.6804 Remote Similarity NPC121825
0.679 Remote Similarity NPC476655
0.679 Remote Similarity NPC476657
0.679 Remote Similarity NPC476654
0.679 Remote Similarity NPC296436
0.679 Remote Similarity NPC176215
0.6786 Remote Similarity NPC476660
0.6782 Remote Similarity NPC470899
0.6778 Remote Similarity NPC286229
0.6774 Remote Similarity NPC258824
0.6747 Remote Similarity NPC209327
0.6747 Remote Similarity NPC273508
0.6742 Remote Similarity NPC477485
0.6737 Remote Similarity NPC14901
0.6737 Remote Similarity NPC159369
0.6737 Remote Similarity NPC130359
0.6737 Remote Similarity NPC39290
0.6731 Remote Similarity NPC251330
0.6709 Remote Similarity NPC321919
0.6709 Remote Similarity NPC81896
0.6707 Remote Similarity NPC476659
0.6707 Remote Similarity NPC476656
0.6706 Remote Similarity NPC477981
0.6706 Remote Similarity NPC477983
0.6705 Remote Similarity NPC477484
0.6705 Remote Similarity NPC477486
0.6703 Remote Similarity NPC11332
0.6703 Remote Similarity NPC180363
0.6703 Remote Similarity NPC73310
0.6703 Remote Similarity NPC94875
0.6703 Remote Similarity NPC473712
0.6703 Remote Similarity NPC473780
0.6703 Remote Similarity NPC65930
0.6703 Remote Similarity NPC475159
0.6703 Remote Similarity NPC131002
0.6703 Remote Similarity NPC329829
0.6703 Remote Similarity NPC473529
0.6703 Remote Similarity NPC145914
0.6701 Remote Similarity NPC469645
0.6701 Remote Similarity NPC469692
0.6667 Remote Similarity NPC473772
0.6667 Remote Similarity NPC77971
0.6667 Remote Similarity NPC260396
0.6667 Remote Similarity NPC94488
0.6667 Remote Similarity NPC475879
0.6667 Remote Similarity NPC175614
0.6635 Remote Similarity NPC154601
0.6632 Remote Similarity NPC201046
0.663 Remote Similarity NPC286770
0.663 Remote Similarity NPC284472
0.663 Remote Similarity NPC161045
0.663 Remote Similarity NPC229799
0.663 Remote Similarity NPC253801
0.6629 Remote Similarity NPC11796
0.6629 Remote Similarity NPC218817
0.6628 Remote Similarity NPC144419
0.6625 Remote Similarity NPC321838
0.6596 Remote Similarity NPC204686
0.6596 Remote Similarity NPC210218
0.6596 Remote Similarity NPC134807
0.6596 Remote Similarity NPC477010
0.6596 Remote Similarity NPC308412
0.6596 Remote Similarity NPC219498
0.6596 Remote Similarity NPC473687
0.6596 Remote Similarity NPC477015
0.6596 Remote Similarity NPC469483
0.6596 Remote Similarity NPC134885
0.6596 Remote Similarity NPC261721
0.6588 Remote Similarity NPC291062
0.6588 Remote Similarity NPC94743
0.6569 Remote Similarity NPC472753
0.6559 Remote Similarity NPC156804
0.6559 Remote Similarity NPC163093
0.6559 Remote Similarity NPC474251
0.6552 Remote Similarity NPC227396
0.6548 Remote Similarity NPC263382
0.6548 Remote Similarity NPC125578
0.6548 Remote Similarity NPC146376
0.6548 Remote Similarity NPC134385
0.6543 Remote Similarity NPC54925
0.6535 Remote Similarity NPC161855
0.6526 Remote Similarity NPC179659
0.6526 Remote Similarity NPC477012
0.6522 Remote Similarity NPC11383
0.6522 Remote Similarity NPC475046
0.6522 Remote Similarity NPC310450
0.6522 Remote Similarity NPC474959
0.6522 Remote Similarity NPC474312
0.6517 Remote Similarity NPC176329
0.6517 Remote Similarity NPC51809
0.6517 Remote Similarity NPC474818
0.6517 Remote Similarity NPC49302
0.6517 Remote Similarity NPC125365
0.6517 Remote Similarity NPC473536
0.6505 Remote Similarity NPC472754
0.6505 Remote Similarity NPC128501
0.65 Remote Similarity NPC229252
0.65 Remote Similarity NPC143857
0.65 Remote Similarity NPC473291
0.6495 Remote Similarity NPC471399
0.6495 Remote Similarity NPC477684
0.6489 Remote Similarity NPC470400
0.6489 Remote Similarity NPC1083
0.6489 Remote Similarity NPC235809
0.6489 Remote Similarity NPC132496
0.6489 Remote Similarity NPC475268
0.6489 Remote Similarity NPC223871
0.6489 Remote Similarity NPC473671
0.6489 Remote Similarity NPC319036
0.6489 Remote Similarity NPC477013
0.6489 Remote Similarity NPC100921
0.6489 Remote Similarity NPC286338
0.6489 Remote Similarity NPC39167
0.6489 Remote Similarity NPC182383
0.6489 Remote Similarity NPC473156
0.6489 Remote Similarity NPC477014
0.6489 Remote Similarity NPC107986
0.6489 Remote Similarity NPC120398
0.6489 Remote Similarity NPC39279
0.6489 Remote Similarity NPC82795
0.6489 Remote Similarity NPC77871
0.6489 Remote Similarity NPC202055
0.6489 Remote Similarity NPC322529
0.6489 Remote Similarity NPC473651
0.6489 Remote Similarity NPC9678
0.6489 Remote Similarity NPC103284
0.6489 Remote Similarity NPC329838
0.6489 Remote Similarity NPC473478
0.6489 Remote Similarity NPC473669
0.6489 Remote Similarity NPC11804
0.6489 Remote Similarity NPC25764
0.6489 Remote Similarity NPC292809
0.6489 Remote Similarity NPC110710
0.6489 Remote Similarity NPC231009
0.6489 Remote Similarity NPC66346
0.6489 Remote Similarity NPC283085
0.6489 Remote Similarity NPC329615
0.6489 Remote Similarity NPC471567
0.6489 Remote Similarity NPC477018
0.6484 Remote Similarity NPC103634
0.6471 Remote Similarity NPC130618
0.6471 Remote Similarity NPC236208
0.6471 Remote Similarity NPC262673
0.6463 Remote Similarity NPC68343
0.6463 Remote Similarity NPC476658
0.6463 Remote Similarity NPC328089
0.6452 Remote Similarity NPC16488
0.6444 Remote Similarity NPC473471
0.6444 Remote Similarity NPC221095
0.6444 Remote Similarity NPC279214
0.6444 Remote Similarity NPC182292
0.6442 Remote Similarity NPC472755
0.6437 Remote Similarity NPC470435
0.6429 Remote Similarity NPC243272
0.6429 Remote Similarity NPC296361
0.6429 Remote Similarity NPC473357
0.6429 Remote Similarity NPC99619
0.6429 Remote Similarity NPC193029
0.6429 Remote Similarity NPC26500
0.6421 Remote Similarity NPC25703
0.6421 Remote Similarity NPC134865
0.6421 Remote Similarity NPC231096
0.6421 Remote Similarity NPC47937
0.6421 Remote Similarity NPC232555
0.6421 Remote Similarity NPC293136
0.6421 Remote Similarity NPC279267
0.6421 Remote Similarity NPC241360
0.6421 Remote Similarity NPC132940
0.6421 Remote Similarity NPC114694
0.6421 Remote Similarity NPC171174
0.6421 Remote Similarity NPC240695

  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 NPC477487 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
0.759 Intermediate Similarity NPD818 Approved
0.759 Intermediate Similarity NPD819 Approved
0.6883 Remote Similarity NPD6109 Phase 1
0.6875 Remote Similarity NPD3197 Phase 1
0.6517 Remote Similarity NPD4756 Discovery
0.631 Remote Similarity NPD3704 Approved
0.6264 Remote Similarity NPD3732 Approved
0.6176 Remote Similarity NPD7839 Suspended
0.6162 Remote Similarity NPD6698 Approved
0.6162 Remote Similarity NPD46 Approved
0.6145 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6118 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6105 Remote Similarity NPD6110 Phase 1
0.61 Remote Similarity NPD7983 Approved
0.6064 Remote Similarity NPD5369 Approved
0.604 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6036 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6036 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5979 Remote Similarity NPD5363 Approved
0.5963 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5957 Remote Similarity NPD4252 Approved
0.5949 Remote Similarity NPD3196 Approved
0.5949 Remote Similarity NPD3195 Phase 2
0.5949 Remote Similarity NPD4266 Approved
0.5949 Remote Similarity NPD3194 Approved
0.5913 Remote Similarity NPD7500 Approved
0.5904 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5865 Remote Similarity NPD4228 Discovery
0.5842 Remote Similarity NPD5785 Approved
0.5833 Remote Similarity NPD6435 Approved
0.5833 Remote Similarity NPD2258 Approved
0.5833 Remote Similarity NPD4269 Approved
0.5833 Remote Similarity NPD4270 Approved
0.5833 Remote Similarity NPD2259 Approved
0.5833 Remote Similarity NPD5209 Approved
0.5823 Remote Similarity NPD3172 Approved
0.581 Remote Similarity NPD6084 Phase 2
0.581 Remote Similarity NPD6083 Phase 2
0.58 Remote Similarity NPD6672 Approved
0.58 Remote Similarity NPD5737 Approved
0.5789 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5773 Remote Similarity NPD7154 Phase 3
0.5769 Remote Similarity NPD5695 Phase 3
0.5763 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5758 Remote Similarity NPD5786 Approved
0.575 Remote Similarity NPD3728 Approved
0.575 Remote Similarity NPD3730 Approved
0.5747 Remote Similarity NPD7331 Phase 2
0.5745 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5743 Remote Similarity NPD6101 Approved
0.5743 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5732 Remote Similarity NPD8779 Phase 3
0.5714 Remote Similarity NPD6413 Approved
0.5714 Remote Similarity NPD3173 Approved
0.5686 Remote Similarity NPD7838 Discovery
0.5682 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5673 Remote Similarity NPD5282 Discontinued
0.5673 Remote Similarity NPD7748 Approved
0.5664 Remote Similarity NPD6421 Discontinued
0.5664 Remote Similarity NPD6371 Approved
0.5656 Remote Similarity NPD4816 Clinical (unspecified phase)
0.5632 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5631 Remote Similarity NPD6411 Approved
0.5625 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5368 Approved
0.5619 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5612 Remote Similarity NPD5362 Discontinued
0.5607 Remote Similarity NPD4225 Approved
0.5607 Remote Similarity NPD5696 Approved
0.5604 Remote Similarity NPD2256 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