Structure

Physi-Chem Properties

Molecular Weight:  223.19
Volume:  262.578
LogP:  3.022
LogD:  2.372
LogS:  -2.458
# Rotatable Bonds:  8
TPSA:  43.09
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.494
Synthetic Accessibility Score:  2.805
Fsp3:  0.643
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:  -4.64
MDCK Permeability:  2.2890906620887108e-05
Pgp-inhibitor:  0.17
Pgp-substrate:  0.024
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.529
30% Bioavailability (F30%):  0.087

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  93.02356719970703%
Volume Distribution (VD):  0.997
Pgp-substrate:  12.809036254882812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.754
CYP1A2-substrate:  0.838
CYP2C19-inhibitor:  0.451
CYP2C19-substrate:  0.449
CYP2C9-inhibitor:  0.445
CYP2C9-substrate:  0.747
CYP2D6-inhibitor:  0.17
CYP2D6-substrate:  0.741
CYP3A4-inhibitor:  0.235
CYP3A4-substrate:  0.209

ADMET: Excretion

Clearance (CL):  5.68
Half-life (T1/2):  0.545

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.505
Drug-inuced Liver Injury (DILI):  0.016
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.015
Maximum Recommended Daily Dose:  0.523
Skin Sensitization:  0.955
Carcinogencity:  0.166
Eye Corrosion:  0.068
Eye Irritation:  0.827
Respiratory Toxicity:  0.024

Download Data

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

  Natural Product: NPC4881

Natural Product ID:  NPC4881
Common Name*:   Gymnamide
IUPAC Name:   (2E,4E,6R)-4,6-dimethyldodeca-2,4-dienamide
Synonyms:   Gymnamide
Standard InCHIKey:  SQTPXUBCYVVRHH-FHYDJSHKSA-N
Standard InCHI:  InChI=1S/C14H25NO/c1-4-5-6-7-8-12(2)11-13(3)9-10-14(15)16/h9-12H,4-8H2,1-3H3,(H2,15,16)/b10-9+,13-11+/t12-/m1/s1
SMILES:  CCCCCC[C@@H](C)/C=C(C)/C=C/C(=N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL443412
PubChem CID:   16091097
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0000475] Carboxylic acid amides
            • [CHEMONTID:0001662] Primary carboxylic acid amides

*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
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[17067147]
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[17988094]
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[18284207]
NPO33119 gymnascella dankaliensis Species Gymnoascaceae Eukaryota n.a. n.a. n.a. PMID[25600409]

☑ 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
NPT168 Cell Line P388 Mus musculus ED50 > 10.0 ug ml-1 PMID[543778]

☑ 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 NPC4881 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
0.8462 Intermediate Similarity NPC91044
0.807 Intermediate Similarity NPC273023
0.7931 Intermediate Similarity NPC104138
0.7931 Intermediate Similarity NPC24216
0.7931 Intermediate Similarity NPC261158
0.7931 Intermediate Similarity NPC306420
0.7857 Intermediate Similarity NPC195986
0.7759 Intermediate Similarity NPC297020
0.7719 Intermediate Similarity NPC303672
0.75 Intermediate Similarity NPC267692
0.75 Intermediate Similarity NPC307435
0.7458 Intermediate Similarity NPC471992
0.7368 Intermediate Similarity NPC243539
0.7368 Intermediate Similarity NPC54542
0.7368 Intermediate Similarity NPC304223
0.7368 Intermediate Similarity NPC145032
0.7368 Intermediate Similarity NPC267340
0.7258 Intermediate Similarity NPC312826
0.7167 Intermediate Similarity NPC471991
0.7119 Intermediate Similarity NPC119655
0.7049 Intermediate Similarity NPC477049
0.7 Intermediate Similarity NPC124382
0.7 Intermediate Similarity NPC13011
0.7 Intermediate Similarity NPC163912
0.7 Intermediate Similarity NPC123669
0.7 Intermediate Similarity NPC167759
0.7 Intermediate Similarity NPC305288
0.7 Intermediate Similarity NPC56028
0.6949 Remote Similarity NPC208638
0.6897 Remote Similarity NPC26960
0.6897 Remote Similarity NPC182102
0.6875 Remote Similarity NPC6795
0.6866 Remote Similarity NPC187315
0.678 Remote Similarity NPC261571
0.6774 Remote Similarity NPC55412
0.6774 Remote Similarity NPC249645
0.6721 Remote Similarity NPC246519
0.6721 Remote Similarity NPC184014
0.6721 Remote Similarity NPC44193
0.6721 Remote Similarity NPC132669
0.6721 Remote Similarity NPC269800
0.6721 Remote Similarity NPC14234
0.6716 Remote Similarity NPC477525
0.6667 Remote Similarity NPC188341
0.6667 Remote Similarity NPC68014
0.6667 Remote Similarity NPC49494
0.6615 Remote Similarity NPC130807
0.6615 Remote Similarity NPC176621
0.6615 Remote Similarity NPC309877
0.6613 Remote Similarity NPC329686
0.6515 Remote Similarity NPC469728
0.65 Remote Similarity NPC244038
0.6406 Remote Similarity NPC245650
0.6349 Remote Similarity NPC474644
0.6316 Remote Similarity NPC138935
0.6269 Remote Similarity NPC324077
0.6269 Remote Similarity NPC329416
0.6269 Remote Similarity NPC317025
0.6269 Remote Similarity NPC326645
0.6269 Remote Similarity NPC317177
0.6269 Remote Similarity NPC29468
0.6269 Remote Similarity NPC225342
0.625 Remote Similarity NPC474643
0.625 Remote Similarity NPC88079
0.625 Remote Similarity NPC194586
0.625 Remote Similarity NPC51758
0.625 Remote Similarity NPC108494
0.625 Remote Similarity NPC473865
0.625 Remote Similarity NPC209279
0.625 Remote Similarity NPC177470
0.625 Remote Similarity NPC180871
0.625 Remote Similarity NPC68889
0.625 Remote Similarity NPC67761
0.6232 Remote Similarity NPC308844
0.6203 Remote Similarity NPC14326
0.6176 Remote Similarity NPC471023
0.6154 Remote Similarity NPC11130
0.6143 Remote Similarity NPC129995
0.6143 Remote Similarity NPC315141
0.6129 Remote Similarity NPC294358
0.6129 Remote Similarity NPC40417
0.6111 Remote Similarity NPC239039
0.6111 Remote Similarity NPC266298
0.6102 Remote Similarity NPC180575
0.6087 Remote Similarity NPC110241
0.6087 Remote Similarity NPC150162
0.6071 Remote Similarity NPC218918
0.6071 Remote Similarity NPC144023
0.6071 Remote Similarity NPC120926
0.6061 Remote Similarity NPC210999
0.6061 Remote Similarity NPC181872
0.6038 Remote Similarity NPC282119
0.6032 Remote Similarity NPC476679
0.6026 Remote Similarity NPC314854
0.6026 Remote Similarity NPC313911
0.6 Remote Similarity NPC187619
0.6 Remote Similarity NPC255042
0.6 Remote Similarity NPC29091
0.6 Remote Similarity NPC477866
0.6 Remote Similarity NPC182840
0.6 Remote Similarity NPC15934
0.6 Remote Similarity NPC103213
0.6 Remote Similarity NPC477865
0.5972 Remote Similarity NPC249713
0.597 Remote Similarity NPC122239
0.597 Remote Similarity NPC309825
0.5965 Remote Similarity NPC206906
0.5942 Remote Similarity NPC182758
0.5942 Remote Similarity NPC174956
0.5942 Remote Similarity NPC77891
0.5932 Remote Similarity NPC269074
0.5915 Remote Similarity NPC255781
0.5902 Remote Similarity NPC106990
0.5893 Remote Similarity NPC56917
0.5893 Remote Similarity NPC183670
0.5882 Remote Similarity NPC47840
0.5882 Remote Similarity NPC471081
0.5882 Remote Similarity NPC234264
0.5882 Remote Similarity NPC240506
0.5873 Remote Similarity NPC157781
0.5873 Remote Similarity NPC181255
0.5873 Remote Similarity NPC306195
0.5873 Remote Similarity NPC35519
0.5873 Remote Similarity NPC179169
0.5873 Remote Similarity NPC35756
0.5867 Remote Similarity NPC314678
0.5862 Remote Similarity NPC470439
0.5857 Remote Similarity NPC300593
0.5857 Remote Similarity NPC253468
0.5857 Remote Similarity NPC235311
0.5846 Remote Similarity NPC298299
0.5846 Remote Similarity NPC130209
0.5846 Remote Similarity NPC148163
0.5846 Remote Similarity NPC251666
0.5846 Remote Similarity NPC148216
0.5846 Remote Similarity NPC227135
0.5846 Remote Similarity NPC232247
0.5833 Remote Similarity NPC254886
0.5833 Remote Similarity NPC278895
0.5821 Remote Similarity NPC155025
0.5806 Remote Similarity NPC329773
0.5806 Remote Similarity NPC474460
0.5802 Remote Similarity NPC224072
0.5802 Remote Similarity NPC39966
0.5797 Remote Similarity NPC210346
0.5789 Remote Similarity NPC269823
0.5789 Remote Similarity NPC188596
0.5783 Remote Similarity NPC3210
0.5735 Remote Similarity NPC150505
0.5735 Remote Similarity NPC475931
0.5735 Remote Similarity NPC74617
0.5714 Remote Similarity NPC474495
0.5714 Remote Similarity NPC26906
0.5714 Remote Similarity NPC473759
0.5714 Remote Similarity NPC474155
0.5714 Remote Similarity NPC214584
0.5714 Remote Similarity NPC55068
0.5714 Remote Similarity NPC81615
0.5714 Remote Similarity NPC59408
0.5714 Remote Similarity NPC473672
0.5714 Remote Similarity NPC124112
0.5714 Remote Similarity NPC71053
0.5714 Remote Similarity NPC473508
0.5694 Remote Similarity NPC308294
0.5694 Remote Similarity NPC142423
0.5694 Remote Similarity NPC267027
0.5694 Remote Similarity NPC230107
0.569 Remote Similarity NPC304151
0.569 Remote Similarity NPC213538
0.569 Remote Similarity NPC256766
0.5676 Remote Similarity NPC90115
0.5676 Remote Similarity NPC239373
0.5676 Remote Similarity NPC45060
0.5676 Remote Similarity NPC471022
0.5676 Remote Similarity NPC217570
0.5676 Remote Similarity NPC329989
0.5676 Remote Similarity NPC280065
0.5667 Remote Similarity NPC24824
0.5667 Remote Similarity NPC165651
0.5667 Remote Similarity NPC210560
0.5667 Remote Similarity NPC299114
0.5652 Remote Similarity NPC99487
0.5652 Remote Similarity NPC66020
0.5647 Remote Similarity NPC473031
0.5645 Remote Similarity NPC31194
0.5645 Remote Similarity NPC248884
0.5645 Remote Similarity NPC85079
0.5634 Remote Similarity NPC475704
0.5625 Remote Similarity NPC71506
0.5625 Remote Similarity NPC177112
0.5625 Remote Similarity NPC471597
0.5604 Remote Similarity NPC167419
0.56 Remote Similarity NPC316029

  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 NPC4881 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
0.6774 Remote Similarity NPD4219 Approved
0.6269 Remote Similarity NPD4192 Approved
0.6269 Remote Similarity NPD4194 Approved
0.6269 Remote Similarity NPD4191 Approved
0.6269 Remote Similarity NPD4193 Approved
0.5938 Remote Similarity NPD9652 Approved
0.5902 Remote Similarity NPD4220 Pre-registration
0.5846 Remote Similarity NPD342 Phase 1
0.5714 Remote Similarity NPD3210 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