Structure

Physi-Chem Properties

Molecular Weight:  130.1
Volume:  144.572
LogP:  2.335
LogD:  1.857
LogS:  -1.605
# Rotatable Bonds:  4
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.631
Synthetic Accessibility Score:  2.292
Fsp3:  0.857
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.516
MDCK Permeability:  2.8932421628269367e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.978
Plasma Protein Binding (PPB):  82.16344451904297%
Volume Distribution (VD):  0.373
Pgp-substrate:  22.994861602783203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.616
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.688
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.898
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.226
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.056

ADMET: Excretion

Clearance (CL):  4.572
Half-life (T1/2):  0.808

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.072
Drug-inuced Liver Injury (DILI):  0.107
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.226
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.256
Carcinogencity:  0.064
Eye Corrosion:  0.983
Eye Irritation:  0.993
Respiratory Toxicity:  0.14

Download Data

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

  Natural Product: NPC252843

Natural Product ID:  NPC252843
Common Name*:   2-Methylhexanoic Acid
IUPAC Name:   2-methylhexanoic acid
Synonyms:  
Standard InCHIKey:  CVKMFSAVYPAZTQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H14O2/c1-3-4-5-6(2)7(8)9/h6H,3-5H2,1-2H3,(H,8,9)
SMILES:  CC(C(=O)O)CCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1789229
PubChem CID:   20653
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
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. PMID[11473446]
NPO22234 Ficus carica Species Moraceae Eukaryota Fruits n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22234 Ficus carica Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22234 Ficus carica Species Moraceae 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 Potency n.a. 19496.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 76958.8 nM PubChem BioAssay data set

☑ 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 NPC252843 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
0.8947 High Similarity NPC325452
0.8947 High Similarity NPC248763
0.8824 High Similarity NPC175342
0.8421 Intermediate Similarity NPC3531
0.8293 Intermediate Similarity NPC55023
0.8286 Intermediate Similarity NPC328710
0.8286 Intermediate Similarity NPC18224
0.8158 Intermediate Similarity NPC38930
0.8158 Intermediate Similarity NPC325454
0.8108 Intermediate Similarity NPC155263
0.8095 Intermediate Similarity NPC314679
0.8 Intermediate Similarity NPC280532
0.7941 Intermediate Similarity NPC122768
0.7941 Intermediate Similarity NPC151140
0.7941 Intermediate Similarity NPC174368
0.7941 Intermediate Similarity NPC61066
0.7941 Intermediate Similarity NPC104195
0.7907 Intermediate Similarity NPC21844
0.7895 Intermediate Similarity NPC109026
0.7838 Intermediate Similarity NPC317203
0.7727 Intermediate Similarity NPC324793
0.7727 Intermediate Similarity NPC477878
0.7692 Intermediate Similarity NPC73245
0.7632 Intermediate Similarity NPC134782
0.75 Intermediate Similarity NPC279026
0.75 Intermediate Similarity NPC201844
0.75 Intermediate Similarity NPC261080
0.75 Intermediate Similarity NPC154186
0.75 Intermediate Similarity NPC301696
0.75 Intermediate Similarity NPC14227
0.75 Intermediate Similarity NPC301585
0.75 Intermediate Similarity NPC113928
0.725 Intermediate Similarity NPC268826
0.7209 Intermediate Similarity NPC319680
0.7143 Intermediate Similarity NPC149184
0.7143 Intermediate Similarity NPC216630
0.7143 Intermediate Similarity NPC163746
0.7143 Intermediate Similarity NPC171736
0.7143 Intermediate Similarity NPC307783
0.7143 Intermediate Similarity NPC103286
0.7143 Intermediate Similarity NPC196924
0.7143 Intermediate Similarity NPC209970
0.7105 Intermediate Similarity NPC127142
0.7105 Intermediate Similarity NPC307027
0.7105 Intermediate Similarity NPC57499
0.7105 Intermediate Similarity NPC7814
0.7073 Intermediate Similarity NPC214610
0.7073 Intermediate Similarity NPC183424
0.7073 Intermediate Similarity NPC118968
0.7073 Intermediate Similarity NPC81263
0.7073 Intermediate Similarity NPC294085
0.7059 Intermediate Similarity NPC149209
0.7059 Intermediate Similarity NPC230726
0.7 Intermediate Similarity NPC14608
0.7 Intermediate Similarity NPC158179
0.6977 Remote Similarity NPC289686
0.6977 Remote Similarity NPC71317
0.6977 Remote Similarity NPC67462
0.6977 Remote Similarity NPC129972
0.6977 Remote Similarity NPC301528
0.6939 Remote Similarity NPC72722
0.6923 Remote Similarity NPC316685
0.6923 Remote Similarity NPC156630
0.6905 Remote Similarity NPC240109
0.6889 Remote Similarity NPC282440
0.6889 Remote Similarity NPC308301
0.6842 Remote Similarity NPC125575
0.6818 Remote Similarity NPC255837
0.6818 Remote Similarity NPC74845
0.6818 Remote Similarity NPC19305
0.6809 Remote Similarity NPC476469
0.675 Remote Similarity NPC154642
0.675 Remote Similarity NPC80396
0.6739 Remote Similarity NPC249754
0.6667 Remote Similarity NPC8219
0.6591 Remote Similarity NPC310220
0.6585 Remote Similarity NPC206924
0.6571 Remote Similarity NPC314668
0.6538 Remote Similarity NPC473936
0.6531 Remote Similarity NPC48162
0.6531 Remote Similarity NPC155512
0.6522 Remote Similarity NPC12438
0.6522 Remote Similarity NPC30195
0.65 Remote Similarity NPC289344
0.65 Remote Similarity NPC155872
0.6458 Remote Similarity NPC162620
0.6458 Remote Similarity NPC62045
0.6458 Remote Similarity NPC245027
0.6444 Remote Similarity NPC323974
0.6429 Remote Similarity NPC54980
0.6429 Remote Similarity NPC22903
0.6429 Remote Similarity NPC305660
0.6429 Remote Similarity NPC316546
0.6429 Remote Similarity NPC201622
0.641 Remote Similarity NPC94196
0.6389 Remote Similarity NPC100997
0.6383 Remote Similarity NPC328497
0.6383 Remote Similarity NPC324004
0.6327 Remote Similarity NPC305182
0.6316 Remote Similarity NPC21374
0.6279 Remote Similarity NPC219536
0.6279 Remote Similarity NPC94368
0.6279 Remote Similarity NPC222792
0.6279 Remote Similarity NPC80234
0.6279 Remote Similarity NPC31551
0.6279 Remote Similarity NPC316217
0.625 Remote Similarity NPC131770
0.625 Remote Similarity NPC106872
0.625 Remote Similarity NPC200618
0.625 Remote Similarity NPC248190
0.625 Remote Similarity NPC154396
0.62 Remote Similarity NPC314084
0.62 Remote Similarity NPC322946
0.619 Remote Similarity NPC317945
0.6182 Remote Similarity NPC475821
0.6182 Remote Similarity NPC470363
0.617 Remote Similarity NPC166287
0.617 Remote Similarity NPC133771
0.6136 Remote Similarity NPC28598
0.6136 Remote Similarity NPC149299
0.6136 Remote Similarity NPC250028
0.6136 Remote Similarity NPC12156
0.6136 Remote Similarity NPC256163
0.6136 Remote Similarity NPC161097
0.6136 Remote Similarity NPC40597
0.6122 Remote Similarity NPC84636
0.6122 Remote Similarity NPC174246
0.6122 Remote Similarity NPC226027
0.6122 Remote Similarity NPC149821
0.6122 Remote Similarity NPC5413
0.6122 Remote Similarity NPC43204
0.6122 Remote Similarity NPC304162
0.6111 Remote Similarity NPC319279
0.6098 Remote Similarity NPC121215
0.6087 Remote Similarity NPC317128
0.6078 Remote Similarity NPC216407
0.6071 Remote Similarity NPC472328
0.6053 Remote Similarity NPC292641
0.6053 Remote Similarity NPC248139
0.6 Remote Similarity NPC41007
0.6 Remote Similarity NPC322892
0.6 Remote Similarity NPC90904
0.6 Remote Similarity NPC286695
0.6 Remote Similarity NPC35371
0.6 Remote Similarity NPC53541
0.6 Remote Similarity NPC178643
0.6 Remote Similarity NPC168714
0.5952 Remote Similarity NPC80641
0.5946 Remote Similarity NPC39869
0.5946 Remote Similarity NPC276332
0.5918 Remote Similarity NPC207292
0.5918 Remote Similarity NPC180534
0.5909 Remote Similarity NPC223249
0.5897 Remote Similarity NPC320981
0.5897 Remote Similarity NPC241404
0.5897 Remote Similarity NPC198126
0.5893 Remote Similarity NPC469924
0.5882 Remote Similarity NPC470411
0.5882 Remote Similarity NPC28205
0.5882 Remote Similarity NPC284212
0.5882 Remote Similarity NPC470412
0.5882 Remote Similarity NPC181153
0.5882 Remote Similarity NPC470410
0.587 Remote Similarity NPC236579
0.587 Remote Similarity NPC176500
0.587 Remote Similarity NPC203531
0.5862 Remote Similarity NPC474552
0.5854 Remote Similarity NPC283682
0.5849 Remote Similarity NPC87394
0.5849 Remote Similarity NPC319589
0.5833 Remote Similarity NPC307594
0.5833 Remote Similarity NPC28246
0.58 Remote Similarity NPC316231
0.58 Remote Similarity NPC112890
0.58 Remote Similarity NPC324825
0.58 Remote Similarity NPC26253
0.5789 Remote Similarity NPC317739
0.5789 Remote Similarity NPC469921
0.5789 Remote Similarity NPC287782
0.5789 Remote Similarity NPC281943
0.5789 Remote Similarity NPC236709
0.5778 Remote Similarity NPC165533
0.5769 Remote Similarity NPC281245
0.5769 Remote Similarity NPC92114
0.5763 Remote Similarity NPC470325
0.5763 Remote Similarity NPC314103
0.5763 Remote Similarity NPC53642
0.5763 Remote Similarity NPC234767
0.575 Remote Similarity NPC12904
0.575 Remote Similarity NPC40965
0.575 Remote Similarity NPC212144
0.575 Remote Similarity NPC328569
0.5745 Remote Similarity NPC76051
0.5745 Remote Similarity NPC132307
0.5745 Remote Similarity NPC325097
0.5745 Remote Similarity NPC126925
0.5741 Remote Similarity NPC67367
0.5714 Remote Similarity NPC191084
0.5714 Remote Similarity NPC168052
0.5714 Remote Similarity NPC250870

  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 NPC252843 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
0.8421 Intermediate Similarity NPD9450 Approved
0.8421 Intermediate Similarity NPD77 Approved
0.8378 Intermediate Similarity NPD9449 Clinical (unspecified phase)
0.8205 Intermediate Similarity NPD9635 Discontinued
0.8095 Intermediate Similarity NPD634 Phase 3
0.7838 Intermediate Similarity NPD9447 Approved
0.75 Intermediate Similarity NPD9448 Phase 2
0.75 Intermediate Similarity NPD633 Phase 3
0.7333 Intermediate Similarity NPD2266 Phase 2
0.7143 Intermediate Similarity NPD2270 Approved
0.7105 Intermediate Similarity NPD8857 Approved
0.7083 Intermediate Similarity NPD3186 Phase 1
0.7073 Intermediate Similarity NPD9655 Approved
0.6977 Remote Similarity NPD387 Clinical (unspecified phase)
0.6875 Remote Similarity NPD9638 Phase 2
0.6818 Remote Similarity NPD8975 Clinical (unspecified phase)
0.68 Remote Similarity NPD615 Clinical (unspecified phase)
0.6744 Remote Similarity NPD9116 Phase 1
0.6667 Remote Similarity NPD8974 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9454 Approved
0.6667 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6471 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6458 Remote Similarity NPD9018 Approved
0.6444 Remote Similarity NPD9019 Approved
0.6429 Remote Similarity NPD3206 Approved
0.6389 Remote Similarity NPD8990 Clinical (unspecified phase)
0.62 Remote Similarity NPD9441 Phase 2
0.6182 Remote Similarity NPD3198 Approved
0.617 Remote Similarity NPD9431 Approved
0.617 Remote Similarity NPD9430 Approved
0.6122 Remote Similarity NPD8946 Approved
0.6122 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6122 Remote Similarity NPD9017 Approved
0.6122 Remote Similarity NPD3173 Approved
0.6122 Remote Similarity NPD8947 Approved
0.6111 Remote Similarity NPD9439 Approved
0.6111 Remote Similarity NPD9438 Approved
0.6053 Remote Similarity NPD62 Approved
0.5965 Remote Similarity NPD9676 Phase 3
0.5918 Remote Similarity NPD622 Approved
0.5897 Remote Similarity NPD8618 Approved
0.5897 Remote Similarity NPD8590 Approved
0.5882 Remote Similarity NPD8201 Phase 2
0.5882 Remote Similarity NPD8615 Phase 2
0.5882 Remote Similarity NPD8616 Clinical (unspecified phase)
0.5814 Remote Similarity NPD9111 Approved
0.5814 Remote Similarity NPD9113 Discontinued
0.5814 Remote Similarity NPD9117 Approved
0.58 Remote Similarity NPD9044 Approved
0.5789 Remote Similarity NPD8594 Approved
0.5789 Remote Similarity NPD8593 Approved
0.5763 Remote Similarity NPD7909 Approved
0.5745 Remote Similarity NPD8798 Approved
0.5714 Remote Similarity NPD8850 Approved
0.5682 Remote Similarity NPD9513 Phase 1
0.566 Remote Similarity NPD3172 Approved
0.5641 Remote Similarity NPD8619 Approved
0.5641 Remote Similarity NPD8617 Approved
0.5625 Remote Similarity NPD2699 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