Structure

Physi-Chem Properties

Molecular Weight:  215.19
Volume:  242.049
LogP:  0.635
LogD:  1.327
LogS:  -2.425
# Rotatable Bonds:  11
TPSA:  63.32
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.521
Synthetic Accessibility Score:  1.763
Fsp3:  0.917
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.485
MDCK Permeability:  1.424851143383421e-05
Pgp-inhibitor:  0.035
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.061
20% Bioavailability (F20%):  0.04
30% Bioavailability (F30%):  0.926

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.975
Plasma Protein Binding (PPB):  59.65559005737305%
Volume Distribution (VD):  0.607
Pgp-substrate:  38.2177734375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.076
CYP1A2-substrate:  0.255
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.127
CYP2C9-inhibitor:  0.04
CYP2C9-substrate:  0.926
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.415
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.035

ADMET: Excretion

Clearance (CL):  3.538
Half-life (T1/2):  0.653

ADMET: Toxicity

hERG Blockers:  0.052
Human Hepatotoxicity (H-HT):  0.158
Drug-inuced Liver Injury (DILI):  0.017
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.494
Maximum Recommended Daily Dose:  0.049
Skin Sensitization:  0.765
Carcinogencity:  0.151
Eye Corrosion:  0.508
Eye Irritation:  0.457
Respiratory Toxicity:  0.937

Download Data

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

  Natural Product: NPC50457

Natural Product ID:  NPC50457
Common Name*:   12-Aminododecanoic Acid
IUPAC Name:   12-azaniumyldodecanoate
Synonyms:   12-Amino-Dodecanoic Acid
Standard InCHIKey:  PBLZLIFKVPJDCO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H25NO2/c13-11-9-7-5-3-1-2-4-6-8-10-12(14)15/h1-11,13H2,(H,14,15)
SMILES:  NCCCCCCCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL371701
PubChem CID:   6997239
69661
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
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[11976110]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[12930985]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[16347440]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[2013566]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[22609920]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25912724]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[28335605]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[28478925]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[8195105]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[9031664]
NPO30084 Pseudomonas sp. Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[9157190]

☑ 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 44668.4 nM PMID[512693]
NPT539 Individual Protein Cellular tumor antigen p53 Homo sapiens Potency n.a. 10000.0 nM PMID[512693]
NPT25074 NUCLEIC-ACID CD40 mRNA n.a. UTC = 68.0 % PMID[512692]
NPT25074 NUCLEIC-ACID CD40 mRNA n.a. UTC = 85.0 % PMID[512692]
NPT25074 NUCLEIC-ACID CD40 mRNA n.a. UTC = 102.0 % PMID[512692]
NPT1 Others Radical scavenging activity Activity = 87.1 % PMID[512694]

☑ 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 NPC50457 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
0.8696 High Similarity NPC323974
0.8 Intermediate Similarity NPC319279
0.7895 Intermediate Similarity NPC302188
0.7843 Intermediate Similarity NPC112890
0.7843 Intermediate Similarity NPC324825
0.7843 Intermediate Similarity NPC316231
0.7708 Intermediate Similarity NPC276294
0.75 Intermediate Similarity NPC278209
0.7447 Intermediate Similarity NPC113928
0.7447 Intermediate Similarity NPC301696
0.7447 Intermediate Similarity NPC279026
0.7447 Intermediate Similarity NPC183424
0.7447 Intermediate Similarity NPC201844
0.7447 Intermediate Similarity NPC294085
0.7447 Intermediate Similarity NPC154186
0.7447 Intermediate Similarity NPC118968
0.7447 Intermediate Similarity NPC214610
0.7447 Intermediate Similarity NPC14227
0.7447 Intermediate Similarity NPC301585
0.7447 Intermediate Similarity NPC261080
0.7368 Intermediate Similarity NPC176164
0.7368 Intermediate Similarity NPC189301
0.7273 Intermediate Similarity NPC183845
0.7273 Intermediate Similarity NPC279661
0.7241 Intermediate Similarity NPC254541
0.7241 Intermediate Similarity NPC320598
0.7234 Intermediate Similarity NPC268826
0.7143 Intermediate Similarity NPC149184
0.7143 Intermediate Similarity NPC216630
0.7143 Intermediate Similarity NPC171736
0.7143 Intermediate Similarity NPC307783
0.7143 Intermediate Similarity NPC196924
0.7143 Intermediate Similarity NPC209970
0.7059 Intermediate Similarity NPC327698
0.7059 Intermediate Similarity NPC118459
0.7 Intermediate Similarity NPC67462
0.6981 Remote Similarity NPC93081
0.6981 Remote Similarity NPC140872
0.6875 Remote Similarity NPC18188
0.6863 Remote Similarity NPC255837
0.6863 Remote Similarity NPC19305
0.6863 Remote Similarity NPC74845
0.6809 Remote Similarity NPC134782
0.6809 Remote Similarity NPC155263
0.6792 Remote Similarity NPC101249
0.6731 Remote Similarity NPC8219
0.6731 Remote Similarity NPC55023
0.6667 Remote Similarity NPC64250
0.6667 Remote Similarity NPC268927
0.6667 Remote Similarity NPC276928
0.6607 Remote Similarity NPC155512
0.6604 Remote Similarity NPC12438
0.6604 Remote Similarity NPC30195
0.6604 Remote Similarity NPC314679
0.6596 Remote Similarity NPC156630
0.6557 Remote Similarity NPC68974
0.6545 Remote Similarity NPC84636
0.6545 Remote Similarity NPC174246
0.6545 Remote Similarity NPC245027
0.6545 Remote Similarity NPC162620
0.6545 Remote Similarity NPC62045
0.6545 Remote Similarity NPC43204
0.6545 Remote Similarity NPC226027
0.6531 Remote Similarity NPC201622
0.6531 Remote Similarity NPC54980
0.6531 Remote Similarity NPC22903
0.6531 Remote Similarity NPC305660
0.6481 Remote Similarity NPC21844
0.6481 Remote Similarity NPC328497
0.6481 Remote Similarity NPC324004
0.6471 Remote Similarity NPC163746
0.6471 Remote Similarity NPC103286
0.6429 Remote Similarity NPC137958
0.6429 Remote Similarity NPC273330
0.6406 Remote Similarity NPC278881
0.64 Remote Similarity NPC31551
0.64 Remote Similarity NPC223249
0.64 Remote Similarity NPC219536
0.6364 Remote Similarity NPC324793
0.6364 Remote Similarity NPC180534
0.6364 Remote Similarity NPC106872
0.6364 Remote Similarity NPC121062
0.6364 Remote Similarity NPC477878
0.6364 Remote Similarity NPC29222
0.6364 Remote Similarity NPC200618
0.6364 Remote Similarity NPC131770
0.6364 Remote Similarity NPC96966
0.6346 Remote Similarity NPC71317
0.6346 Remote Similarity NPC129972
0.6346 Remote Similarity NPC301528
0.6324 Remote Similarity NPC306973
0.6296 Remote Similarity NPC166287
0.6275 Remote Similarity NPC28598
0.6275 Remote Similarity NPC165533
0.6275 Remote Similarity NPC149299
0.6275 Remote Similarity NPC40597
0.6275 Remote Similarity NPC326992
0.6275 Remote Similarity NPC161097
0.6275 Remote Similarity NPC12156
0.6275 Remote Similarity NPC256163
0.6275 Remote Similarity NPC168375
0.6275 Remote Similarity NPC121517
0.6275 Remote Similarity NPC66043
0.6275 Remote Similarity NPC250028
0.625 Remote Similarity NPC304162
0.6212 Remote Similarity NPC314221
0.6212 Remote Similarity NPC60424
0.6207 Remote Similarity NPC190184
0.6207 Remote Similarity NPC474322
0.6207 Remote Similarity NPC123814
0.6207 Remote Similarity NPC197087
0.62 Remote Similarity NPC73245
0.617 Remote Similarity NPC328710
0.617 Remote Similarity NPC18224
0.617 Remote Similarity NPC175342
0.6154 Remote Similarity NPC248763
0.6154 Remote Similarity NPC325452
0.6154 Remote Similarity NPC53541
0.6143 Remote Similarity NPC208657
0.614 Remote Similarity NPC329181
0.614 Remote Similarity NPC319110
0.614 Remote Similarity NPC90904
0.6129 Remote Similarity NPC321536
0.6129 Remote Similarity NPC327748
0.6129 Remote Similarity NPC317143
0.6129 Remote Similarity NPC321468
0.6129 Remote Similarity NPC316826
0.6111 Remote Similarity NPC329263
0.6078 Remote Similarity NPC80234
0.6066 Remote Similarity NPC318260
0.6066 Remote Similarity NPC317147
0.6038 Remote Similarity NPC203531
0.6038 Remote Similarity NPC289686
0.6038 Remote Similarity NPC236579
0.6038 Remote Similarity NPC167986
0.6038 Remote Similarity NPC291186
0.6034 Remote Similarity NPC470412
0.6034 Remote Similarity NPC100096
0.6034 Remote Similarity NPC470410
0.6032 Remote Similarity NPC327170
0.6032 Remote Similarity NPC329564
0.6032 Remote Similarity NPC143722
0.6 Remote Similarity NPC2801
0.6 Remote Similarity NPC315897
0.5974 Remote Similarity NPC199072
0.597 Remote Similarity NPC222327
0.597 Remote Similarity NPC188231
0.5968 Remote Similarity NPC245346
0.5968 Remote Similarity NPC11433
0.5968 Remote Similarity NPC302003
0.5965 Remote Similarity NPC26253
0.5932 Remote Similarity NPC281245
0.5932 Remote Similarity NPC18357
0.5926 Remote Similarity NPC132307
0.5926 Remote Similarity NPC325097
0.5926 Remote Similarity NPC317128
0.5926 Remote Similarity NPC126925
0.5926 Remote Similarity NPC76051
0.5918 Remote Similarity NPC317203
0.5902 Remote Similarity NPC325985
0.5902 Remote Similarity NPC38463
0.5882 Remote Similarity NPC107224
0.5882 Remote Similarity NPC326532
0.5862 Remote Similarity NPC125736
0.5833 Remote Similarity NPC139029
0.5833 Remote Similarity NPC72722
0.5833 Remote Similarity NPC294548
0.5833 Remote Similarity NPC36061
0.5833 Remote Similarity NPC114517
0.5833 Remote Similarity NPC1813
0.5823 Remote Similarity NPC83839
0.5821 Remote Similarity NPC470108
0.5818 Remote Similarity NPC287231
0.5818 Remote Similarity NPC469781
0.5818 Remote Similarity NPC47363
0.5806 Remote Similarity NPC8979
0.5797 Remote Similarity NPC15864
0.5789 Remote Similarity NPC193872
0.5789 Remote Similarity NPC327542
0.5769 Remote Similarity NPC3531
0.5758 Remote Similarity NPC315744
0.5758 Remote Similarity NPC57420
0.5738 Remote Similarity NPC320588
0.5738 Remote Similarity NPC32467
0.5738 Remote Similarity NPC6095
0.5738 Remote Similarity NPC424
0.5738 Remote Similarity NPC469937
0.5738 Remote Similarity NPC154245
0.5738 Remote Similarity NPC25417
0.5738 Remote Similarity NPC53463
0.5738 Remote Similarity NPC290563
0.5738 Remote Similarity NPC88966
0.5738 Remote Similarity NPC23155
0.5738 Remote Similarity NPC261831
0.5738 Remote Similarity NPC87564
0.5738 Remote Similarity NPC87394
0.5738 Remote Similarity NPC281972
0.5738 Remote Similarity NPC85813
0.5735 Remote Similarity NPC470109
0.5714 Remote Similarity NPC190385

  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 NPC50457 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
0.8696 High Similarity NPD9019 Approved
0.807 Intermediate Similarity NPD9676 Phase 3
0.8 Intermediate Similarity NPD9439 Approved
0.8 Intermediate Similarity NPD9438 Approved
0.7895 Intermediate Similarity NPD9656 Approved
0.7843 Intermediate Similarity NPD9044 Approved
0.7843 Intermediate Similarity NPD9016 Clinical (unspecified phase)
0.7636 Intermediate Similarity NPD9454 Approved
0.7447 Intermediate Similarity NPD9655 Approved
0.7447 Intermediate Similarity NPD9448 Phase 2
0.7447 Intermediate Similarity NPD633 Phase 3
0.7143 Intermediate Similarity NPD2270 Approved
0.6984 Remote Similarity NPD375 Phase 2
0.6984 Remote Similarity NPD9421 Phase 1
0.6981 Remote Similarity NPD8808 Approved
0.6981 Remote Similarity NPD8809 Approved
0.697 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6875 Remote Similarity NPD8623 Phase 1
0.6792 Remote Similarity NPD8866 Approved
0.6792 Remote Similarity NPD8867 Approved
0.6765 Remote Similarity NPD632 Discontinued
0.6731 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6604 Remote Similarity NPD634 Phase 3
0.6545 Remote Similarity NPD9017 Approved
0.6545 Remote Similarity NPD9018 Approved
0.6531 Remote Similarity NPD3206 Approved
0.6429 Remote Similarity NPD8872 Phase 3
0.6429 Remote Similarity NPD8871 Approved
0.6389 Remote Similarity NPD617 Approved
0.6379 Remote Similarity NPD630 Approved
0.6379 Remote Similarity NPD631 Approved
0.6364 Remote Similarity NPD622 Approved
0.6364 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6296 Remote Similarity NPD9430 Approved
0.6296 Remote Similarity NPD9431 Approved
0.6207 Remote Similarity NPD8851 Phase 1
0.6207 Remote Similarity NPD3215 Phase 1
0.6207 Remote Similarity NPD8785 Approved
0.6167 Remote Similarity NPD8981 Clinical (unspecified phase)
0.6167 Remote Similarity NPD8979 Approved
0.6167 Remote Similarity NPD8980 Approved
0.614 Remote Similarity NPD3214 Discontinued
0.6061 Remote Similarity NPD9201 Clinical (unspecified phase)
0.6038 Remote Similarity NPD8804 Approved
0.6038 Remote Similarity NPD8805 Approved
0.6038 Remote Similarity NPD387 Clinical (unspecified phase)
0.6 Remote Similarity NPD8971 Approved
0.6 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5974 Remote Similarity NPD326 Approved
0.5968 Remote Similarity NPD9433 Approved
0.5968 Remote Similarity NPD8865 Approved
0.5932 Remote Similarity NPD3186 Phase 1
0.5926 Remote Similarity NPD8798 Approved
0.5926 Remote Similarity NPD9062 Phase 2
0.5921 Remote Similarity NPD857 Phase 3
0.5893 Remote Similarity NPD8973 Approved
0.5893 Remote Similarity NPD8972 Approved
0.5893 Remote Similarity NPD8850 Approved
0.5882 Remote Similarity NPD9513 Phase 1
0.5833 Remote Similarity NPD3172 Approved
0.5818 Remote Similarity NPD2699 Approved
0.5775 Remote Similarity NPD1147 Phase 2
0.5769 Remote Similarity NPD77 Approved
0.5769 Remote Similarity NPD9450 Approved
0.5753 Remote Similarity NPD2257 Approved
0.5738 Remote Similarity NPD3196 Approved
0.5738 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5738 Remote Similarity NPD3195 Phase 2
0.5738 Remote Similarity NPD3194 Approved
0.5738 Remote Similarity NPD615 Clinical (unspecified phase)
0.5738 Remote Similarity NPD3728 Approved
0.5738 Remote Similarity NPD4266 Approved
0.5738 Remote Similarity NPD3730 Approved
0.5733 Remote Similarity NPD3732 Approved
0.5714 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5692 Remote Similarity NPD9014 Approved
0.569 Remote Similarity NPD8946 Approved
0.569 Remote Similarity NPD8947 Approved
0.5679 Remote Similarity NPD621 Discontinued
0.5672 Remote Similarity NPD348 Approved
0.5645 Remote Similarity NPD4281 Clinical (unspecified phase)
0.5634 Remote Similarity NPD5382 Phase 2

  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