Structure

Physi-Chem Properties

Molecular Weight:  285.19
Volume:  312.381
LogP:  3.637
LogD:  4.281
LogS:  -4.413
# Rotatable Bonds:  11
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.574
Synthetic Accessibility Score:  2.877
Fsp3:  0.688
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:  -4.361
MDCK Permeability:  2.874756137316581e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.845
Plasma Protein Binding (PPB):  84.6775131225586%
Volume Distribution (VD):  0.391
Pgp-substrate:  7.741428852081299%

ADMET: Metabolism

CYP1A2-inhibitor:  0.734
CYP1A2-substrate:  0.323
CYP2C19-inhibitor:  0.838
CYP2C19-substrate:  0.248
CYP2C9-inhibitor:  0.652
CYP2C9-substrate:  0.928
CYP2D6-inhibitor:  0.41
CYP2D6-substrate:  0.567
CYP3A4-inhibitor:  0.775
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  4.296
Half-life (T1/2):  0.861

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.302
Drug-inuced Liver Injury (DILI):  0.248
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.14
Skin Sensitization:  0.551
Carcinogencity:  0.134
Eye Corrosion:  0.003
Eye Irritation:  0.074
Respiratory Toxicity:  0.039

Download Data

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

  Natural Product: NPC210999

Natural Product ID:  NPC210999
Common Name*:   Credneramide B
IUPAC Name:   (E,7E)-7-(chloromethylidene)-N-(3-methylbutyl)dec-4-enamide
Synonyms:   Credneramide B
Standard InCHIKey:  WHDZTXRZTFGPRJ-HQYXJCMVSA-N
Standard InCHI:  InChI=1S/C16H28ClNO/c1-4-8-15(13-17)9-6-5-7-10-16(19)18-12-11-14(2)3/h5-6,13-14H,4,7-12H2,1-3H3,(H,18,19)/b6-5+,15-13+
SMILES:  CCC/C(=CCl)/C/C=C/CCC(=NCCC(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1950964
PubChem CID:   57332911
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO32873 Trichodesmium sp. Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[22148360]

☑ 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 IC50 = 3900.0 nM PMID[489593]

☑ 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 NPC210999 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
0.7213 Intermediate Similarity NPC471992
0.7213 Intermediate Similarity NPC242930
0.7167 Intermediate Similarity NPC303672
0.7 Intermediate Similarity NPC195986
0.6935 Remote Similarity NPC297020
0.6935 Remote Similarity NPC273023
0.6875 Remote Similarity NPC321030
0.6875 Remote Similarity NPC325734
0.6833 Remote Similarity NPC145032
0.6833 Remote Similarity NPC267340
0.6833 Remote Similarity NPC54542
0.6833 Remote Similarity NPC243539
0.6833 Remote Similarity NPC304223
0.6825 Remote Similarity NPC261158
0.6825 Remote Similarity NPC104138
0.6825 Remote Similarity NPC24216
0.6825 Remote Similarity NPC477049
0.6825 Remote Similarity NPC306420
0.68 Remote Similarity NPC469492
0.6774 Remote Similarity NPC124382
0.6774 Remote Similarity NPC13011
0.6769 Remote Similarity NPC326524
0.6769 Remote Similarity NPC325550
0.6769 Remote Similarity NPC329003
0.6711 Remote Similarity NPC469517
0.6667 Remote Similarity NPC307435
0.6667 Remote Similarity NPC130807
0.6667 Remote Similarity NPC471991
0.6667 Remote Similarity NPC267692
0.6613 Remote Similarity NPC119655
0.6557 Remote Similarity NPC261571
0.6508 Remote Similarity NPC167759
0.6508 Remote Similarity NPC305288
0.6508 Remote Similarity NPC56028
0.6508 Remote Similarity NPC163912
0.6471 Remote Similarity NPC316674
0.6471 Remote Similarity NPC477106
0.6452 Remote Similarity NPC188341
0.6452 Remote Similarity NPC49494
0.6418 Remote Similarity NPC6795
0.6418 Remote Similarity NPC309877
0.6386 Remote Similarity NPC12429
0.6324 Remote Similarity NPC29468
0.629 Remote Similarity NPC178586
0.6286 Remote Similarity NPC477525
0.6269 Remote Similarity NPC312826
0.625 Remote Similarity NPC123669
0.625 Remote Similarity NPC44193
0.625 Remote Similarity NPC246519
0.625 Remote Similarity NPC269800
0.625 Remote Similarity NPC184014
0.625 Remote Similarity NPC132669
0.625 Remote Similarity NPC14234
0.6232 Remote Similarity NPC471023
0.6207 Remote Similarity NPC470439
0.6061 Remote Similarity NPC4881
0.6027 Remote Similarity NPC249713
0.5972 Remote Similarity NPC129995
0.5972 Remote Similarity NPC187315
0.5972 Remote Similarity NPC315141
0.5946 Remote Similarity NPC291196
0.5946 Remote Similarity NPC103712
0.5921 Remote Similarity NPC314678
0.5862 Remote Similarity NPC188596
0.5857 Remote Similarity NPC273614
0.5854 Remote Similarity NPC39966
0.5854 Remote Similarity NPC224072
0.5806 Remote Similarity NPC91044
0.5797 Remote Similarity NPC74617
0.5797 Remote Similarity NPC150505
0.5769 Remote Similarity NPC264417
0.5769 Remote Similarity NPC217095
0.5763 Remote Similarity NPC88079
0.5763 Remote Similarity NPC180871
0.5763 Remote Similarity NPC194586
0.5763 Remote Similarity NPC68889
0.5763 Remote Similarity NPC108494
0.5763 Remote Similarity NPC67761
0.5763 Remote Similarity NPC209279
0.5763 Remote Similarity NPC51758
0.5738 Remote Similarity NPC210560
0.5738 Remote Similarity NPC24824
0.5738 Remote Similarity NPC165651
0.5735 Remote Similarity NPC245650
0.5733 Remote Similarity NPC45060
0.5733 Remote Similarity NPC280065
0.5733 Remote Similarity NPC471022
0.5714 Remote Similarity NPC477199
0.5694 Remote Similarity NPC235311
0.5694 Remote Similarity NPC253468
0.5679 Remote Similarity NPC157173
0.5679 Remote Similarity NPC471597
0.5641 Remote Similarity NPC288086
0.5634 Remote Similarity NPC21848
0.5634 Remote Similarity NPC124849
0.5634 Remote Similarity NPC324077
0.5632 Remote Similarity NPC316186
0.5625 Remote Similarity NPC329773

  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 NPC210999 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
0.625 Remote Similarity NPD9652 Approved
0.5882 Remote Similarity NPD570 Approved
0.5797 Remote Similarity NPD571 Approved
0.5698 Remote Similarity NPD187 Approved
0.5634 Remote Similarity NPD834 Approved
0.5634 Remote Similarity NPD835 Approved
0.5606 Remote Similarity NPD9575 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