Structure

Physi-Chem Properties

Molecular Weight:  300.1
Volume:  303.515
LogP:  3.13
LogD:  2.222
LogS:  -7.291
# Rotatable Bonds:  0
TPSA:  81.23
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.307
Synthetic Accessibility Score:  2.956
Fsp3:  0.111
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.878
MDCK Permeability:  1.1951085980399512e-05
Pgp-inhibitor:  0.026
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.045
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.17
Plasma Protein Binding (PPB):  92.73499298095703%
Volume Distribution (VD):  1.596
Pgp-substrate:  4.652426719665527%

ADMET: Metabolism

CYP1A2-inhibitor:  0.981
CYP1A2-substrate:  0.685
CYP2C19-inhibitor:  0.164
CYP2C19-substrate:  0.199
CYP2C9-inhibitor:  0.373
CYP2C9-substrate:  0.203
CYP2D6-inhibitor:  0.764
CYP2D6-substrate:  0.853
CYP3A4-inhibitor:  0.273
CYP3A4-substrate:  0.16

ADMET: Excretion

Clearance (CL):  1.932
Half-life (T1/2):  0.085

ADMET: Toxicity

hERG Blockers:  0.195
Human Hepatotoxicity (H-HT):  0.882
Drug-inuced Liver Injury (DILI):  0.985
AMES Toxicity:  0.694
Rat Oral Acute Toxicity:  0.083
Maximum Recommended Daily Dose:  0.938
Skin Sensitization:  0.83
Carcinogencity:  0.818
Eye Corrosion:  0.003
Eye Irritation:  0.08
Respiratory Toxicity:  0.955

Download Data

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

  Natural Product: NPC467022

Natural Product ID:  NPC467022
Common Name*:   Dehydrocrambine A
IUPAC Name:   4-(diaminomethylideneamino)butyl 1-imino-3-undecyl-6,7-dihydro-5H-pyrrolo[1,2-c]pyrimidine-4-carboxylate
Synonyms:  
Standard InCHIKey:  KRUORMCKORWKOO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C24H42N6O2/c1-2-3-4-5-6-7-8-9-10-14-19-21(20-15-13-17-30(20)24(27)29-19)22(31)32-18-12-11-16-28-23(25)26/h27H,2-18H2,1H3,(H4,25,26,28)
SMILES:  CCCCCCCCCCCC1=NC(=N)N2CCCC2=C1C(=O)OCCCCN=C(N)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3011699
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001799] Pyrrolopyrimidines

*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
NPO32454 monanchora sp. Species Crambeidae Eukaryota n.a. n.a. n.a. PMID[14640525]
NPO32454 monanchora sp. Species Crambeidae Eukaryota n.a. Korean n.a. PMID[23360104]
NPO32454 monanchora sp. Species Crambeidae Eukaryota n.a. at 1520 m depth off the shore of Gageo Island, southwestern Korea 2009-JUL PMID[25455409]

☑ 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 = 35000 nM PMID[14640525]

☑ 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 NPC467022 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
0.9333 High Similarity NPC469423
0.8305 Intermediate Similarity NPC469387
0.7561 Intermediate Similarity NPC324722
0.7561 Intermediate Similarity NPC311244
0.7561 Intermediate Similarity NPC198644
0.7064 Intermediate Similarity NPC469424
0.6637 Remote Similarity NPC472736
0.6357 Remote Similarity NPC142761
0.6261 Remote Similarity NPC476449
0.6154 Remote Similarity NPC477519
0.6148 Remote Similarity NPC261730
0.598 Remote Similarity NPC472735
0.597 Remote Similarity NPC473249
0.595 Remote Similarity NPC469895
0.5923 Remote Similarity NPC471261
0.5873 Remote Similarity NPC147238
0.5847 Remote Similarity NPC471257
0.584 Remote Similarity NPC469388
0.584 Remote Similarity NPC469389
0.584 Remote Similarity NPC472737
0.5798 Remote Similarity NPC472162
0.5726 Remote Similarity NPC471259
0.5714 Remote Similarity NPC245534
0.5667 Remote Similarity NPC241426
0.5649 Remote Similarity NPC477121
0.563 Remote Similarity NPC150041
0.5615 Remote Similarity NPC471645
0.5614 Remote Similarity NPC130436
0.5614 Remote Similarity NPC469860
0.5614 Remote Similarity NPC469861
0.561 Remote Similarity NPC471258
0.5603 Remote Similarity NPC304455

  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 NPC467022 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
0.626 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6016 Remote Similarity NPD6935 Phase 3
0.6016 Remote Similarity NPD6936 Clinical (unspecified phase)
0.597 Remote Similarity NPD7747 Phase 1
0.597 Remote Similarity NPD7746 Phase 1
0.5969 Remote Similarity NPD6918 Phase 1
0.5954 Remote Similarity NPD7739 Clinical (unspecified phase)
0.595 Remote Similarity NPD2259 Approved
0.595 Remote Similarity NPD2258 Approved
0.5909 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5909 Remote Similarity NPD7623 Phase 3
0.5692 Remote Similarity NPD869 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