Structure

Physi-Chem Properties

Molecular Weight:  906.4
Volume:  887.783
LogP:  5.837
LogD:  5.09
LogS:  -5.291
# Rotatable Bonds:  0
TPSA:  180.86
# H-Bond Aceptor:  15
# H-Bond Donor:  2
# Rings:  17
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.281
Synthetic Accessibility Score:  8.03
Fsp3:  0.577
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.393
MDCK Permeability:  3.1274415960069746e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.988
20% Bioavailability (F20%):  0.978
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.504
Plasma Protein Binding (PPB):  93.96062469482422%
Volume Distribution (VD):  1.894
Pgp-substrate:  2.7873613834381104%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.284
CYP2C19-inhibitor:  0.636
CYP2C19-substrate:  0.937
CYP2C9-inhibitor:  0.82
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.633
CYP2D6-substrate:  0.018
CYP3A4-inhibitor:  0.978
CYP3A4-substrate:  0.971

ADMET: Excretion

Clearance (CL):  4.219
Half-life (T1/2):  0.013

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.983
Drug-inuced Liver Injury (DILI):  0.951
AMES Toxicity:  0.231
Rat Oral Acute Toxicity:  0.958
Maximum Recommended Daily Dose:  0.986
Skin Sensitization:  0.248
Carcinogencity:  0.98
Eye Corrosion:  0.003
Eye Irritation:  0.004
Respiratory Toxicity:  0.831

Download Data

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

  Natural Product: NPC476648

Natural Product ID:  NPC476648
Common Name*:   (1R,2S,4R,10S,12S,26R,27R,28S,42S,44S)-26-hydroxy-13,13,20,20,34,34,41,41-octamethyl-15,39-dioxido-21,33-dioxa-3,6,48,50-tetraza-15,39-diazoniapentadecacyclo[42.5.2.13,10.01,42.02,28.04,12.04,27.06,10.014,26.016,25.017,22.028,40.029,38.032,37.044,48]dopentaconta-14,16(25),17(22),18,23,29(38),30,32(37),35,39-decaene-5,49,51,52-tetrone
IUPAC Name:   (1R,2S,4R,10S,12S,26R,27R,28S,42S,44S)-26-hydroxy-13,13,20,20,34,34,41,41-octamethyl-15,39-dioxido-21,33-dioxa-3,6,48,50-tetraza-15,39-diazoniapentadecacyclo[42.5.2.13,10.01,42.02,28.04,12.04,27.06,10.014,26.016,25.017,22.028,40.029,38.032,37.044,48]dopentaconta-14,16(25),17(22),18,23,29(38),30,32(37),35,39-decaene-5,49,51,52-tetrone
Synonyms:   Waikialoid B
Standard InCHIKey:  WMVPIWNYGIBPQV-CRWMDOOPSA-N
Standard InCHI:  InChI=1S/C52H54N6O9/c1-43(2)19-15-25-29(66-43)13-11-27-33(25)57(64)36-45(5,6)31-23-47-17-9-21-54(47)41(61)50(31,53-39(47)59)38-49(27,36)35-51-32(24-48(40(60)56(38)51)18-10-22-55(48)42(51)62)46(7,8)37-52(35,63)28-12-14-30-26(34(28)58(37)65)16-20-44(3,4)67-30/h11-16,19-20,31-32,35,38,63H,9-10,17-18,21-24H2,1-8H3,(H,53,59)/t31-,32-,35+,38-,47-,48-,49-,50+,51+,52-/m0/s1
SMILES:  CC1(C=CC2=C(O1)C=CC3=C2[N+](=C4[C@@]35[C@@H]6[C@]78[C@@H](C[C@@]9(CCCN9C7=O)C(=O)N8[C@@H]5[C@]12[C@H](C4(C)C)C[C@@]3(CCCN3C1=O)C(=O)N2)C(C1=[N+](C2=C([C@]61O)C=CC1=C2C=CC(O1)(C)C)[O-])(C)C)[O-])C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   57408409
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0000210] Carbazoles
          • [CHEMONTID:0001865] Pyrrolocarbazoles
            • [CHEMONTID:0001866] Indolocarbazoles

*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
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota rhizosphere Sonoran desert n.a. PMID[15620238]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17542490]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17564467]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19053517]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21366228]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21718031]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21854017]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota healthy leaf of Ginkgo biloba campus of Nanjing University, Nanjing, China 2008-OCT PMID[22196792]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota isolated from the sponge Xestospongia testudinaria n.a. n.a. PMID[22225637]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota Isolated from a sandy-loam soil sample 50 m inland from Waikiki Beach, Honolulu, Hawaii 2010-JUL PMID[22400916]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22703109]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23527875]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24050204]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25001296]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[25581396]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26273902]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31012585]
NPO31572 Aspergillus sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[33305943]

☑ 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
NPT783 Cell Line MIA PaCa-2 Homo sapiens IC50 = 8200 nM PMID[22400916]
NPT20 Organism Candida albicans Candida albicans MIC > 200000 nM PMID[22400916]
NPT20 Organism Candida albicans Candida albicans IC50 = 46300 nM PMID[22400916]

☑ 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 NPC476648 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
NPC

  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 NPC476648 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
NPD

  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