Structure

Physi-Chem Properties

Molecular Weight:  960.53
Volume:  954.39
LogP:  3.069
LogD:  1.035
LogS:  -4.472
# Rotatable Bonds:  2
TPSA:  244.77
# H-Bond Aceptor:  15
# H-Bond Donor:  9
# Rings:  13
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.194
Synthetic Accessibility Score:  5.52
Fsp3:  0.852
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.18
MDCK Permeability:  6.0211081290617585e-05
Pgp-inhibitor:  0.121
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.779
20% Bioavailability (F20%):  0.98
30% Bioavailability (F30%):  0.966

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.17
Plasma Protein Binding (PPB):  61.054481506347656%
Volume Distribution (VD):  0.381
Pgp-substrate:  15.358227729797363%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.939
CYP2C19-inhibitor:  0.001
CYP2C19-substrate:  0.674
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.002
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.075
CYP3A4-inhibitor:  0.902
CYP3A4-substrate:  0.496

ADMET: Excretion

Clearance (CL):  3.553
Half-life (T1/2):  0.199

ADMET: Toxicity

hERG Blockers:  0.591
Human Hepatotoxicity (H-HT):  0.988
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.987
Maximum Recommended Daily Dose:  0.997
Skin Sensitization:  0.645
Carcinogencity:  0.693
Eye Corrosion:  0.003
Eye Irritation:  0.004
Respiratory Toxicity:  0.994

Download Data

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

  Natural Product: NPC471557

Natural Product ID:  NPC471557
Common Name*:   Cephalostatin 13
IUPAC Name:   n.a.
Synonyms:   Cephalostatin 13
Standard InCHIKey:  ZZWDNFAHBZOHKA-PXTNZQIYSA-N
Standard InCHI:  InChI=1S/C54H76N2O13/c1-24-51(64)41(66-53(24)39(61)20-45(3,22-57)68-53)17-32-28-11-9-26-13-34-36(19-47(26,5)30(28)15-37(59)49(32,51)7)55-35-14-27-10-12-29-31(48(27,6)44(63)43(35)56-34)16-38(60)50(8)33(29)18-42-52(50,65)25(2)54(67-42)40(62)21-46(4,23-58)69-54/h17-18,24-31,37-42,44,57-65H,9-16,19-23H2,1-8H3/t24-,25-,26-,27-,28+,29+,30-,31-,37+,38+,39+,40+,41-,42-,44-,45-,46-,47-,48-,49+,50+,51+,52+,53-,54-/m0/s1
SMILES:  OC[C@]1(C)C[C@H]([C@]2(O1)O[C@@H]1[C@@]([C@@H]2C)(O)[C@@]2(C(=C1)[C@@H]1CC[C@@H]3[C@]([C@H]1C[C@H]2O)(C)Cc1c(C3)nc2c(n1)C[C@H]1[C@@]([C@H]2O)(C)[C@H]2C[C@@H](O)[C@]3(C(=C[C@H]4[C@]3(O)[C@H](C)[C@]3(O4)O[C@](C[C@H]3O)(C)CO)[C@@H]2CC1)C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL256953
PubChem CID:   21774831
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001295] Hydroxysteroids
          • [CHEMONTID:0004158] 1-hydroxysteroids

*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
NPO25585 Cephalodiscus gilchristi Species Cephalodiscidae Eukaryota n.a. n.a. n.a. PMID[21899266]
NPO25585 Cephalodiscus gilchristi Species Cephalodiscidae Eukaryota n.a. n.a. n.a. PMID[22607450]
NPO25585 Cephalodiscus gilchristi Species Cephalodiscidae Eukaryota n.a. n.a. 1990 PMID[26042639]
NPO25585 Cephalodiscus gilchristi Species Cephalodiscidae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT4461 Cell Line Panel (Carcinoma cell lines) Homo sapiens ED50 = 0.046 ug ml-1 PMID[470723]
NPT4461 Cell Line Panel (Carcinoma cell lines) Homo sapiens GI50 > 1000.0 nM PMID[470723]
NPT168 Cell Line P388 Mus musculus ED50 = 47.9 nM PMID[470724]
NPT83 Cell Line MCF7 Homo sapiens GI50 = 290.0 nM PMID[470725]
NPT395 Cell Line SF-268 Homo sapiens GI50 = 340.0 nM PMID[470725]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 = 370.0 nM PMID[470725]
NPT90 Cell Line DU-145 Homo sapiens GI50 = 1100.0 nM PMID[470725]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 310.0 nM PMID[470725]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 470.0 nM PMID[470725]

☑ 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 NPC471557 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 NPC471557 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