Structure

Physi-Chem Properties

Molecular Weight:  802.63
Volume:  854.906
LogP:  6.33
LogD:  4.111
LogS:  -5.023
# Rotatable Bonds:  27
TPSA:  164.97
# H-Bond Aceptor:  12
# H-Bond Donor:  6
# Rings:  5
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.056
Synthetic Accessibility Score:  6.071
Fsp3:  0.933
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:  -5.576
MDCK Permeability:  3.531958645908162e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.992
Human Intestinal Absorption (HIA):  0.041
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  80.5620346069336%
Volume Distribution (VD):  0.591
Pgp-substrate:  15.831931114196777%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.262
CYP2C19-inhibitor:  0.228
CYP2C19-substrate:  0.171
CYP2C9-inhibitor:  0.142
CYP2C9-substrate:  0.04
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.127
CYP3A4-inhibitor:  0.963
CYP3A4-substrate:  0.503

ADMET: Excretion

Clearance (CL):  7.405
Half-life (T1/2):  0.008

ADMET: Toxicity

hERG Blockers:  0.586
Human Hepatotoxicity (H-HT):  0.983
Drug-inuced Liver Injury (DILI):  0.02
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.99
Skin Sensitization:  0.972
Carcinogencity:  0.073
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.901

Download Data

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

  Natural Product: NPC477518

Natural Product ID:  NPC477518
Common Name*:   Crambescidin 800
IUPAC Name:   n.a.
Synonyms:   Crambescidin 800
Standard InCHIKey:  CPTIHYXEKGLXRV-BPXWMNIUSA-N
Standard InCHI:  InChI=1S/C45H82N6O6/c1-3-38-22-16-17-27-44(57-38)33-36-24-25-39-41(45(28-19-21-35(2)56-45)49-43(48-44)51(36)39)42(54)55-32-18-14-12-10-8-6-4-5-7-9-11-13-15-23-40(53)50(31-20-29-46)34-37(52)26-30-47/h35-39,41,52H,3-34,46-47H2,1-2H3,(H,48,49)/t35-,36+,37+,38+,39-,41-,44+,45-/m1/s1
SMILES:  CC[C@H]1CCCC[C@]2(O1)C[C@@H]3CC[C@H]4N3C(=N[C@]5([C@H]4C(=O)OCCCCCCCCCCCCCCCC(=O)N(CCCN)C[C@H](CCN)O)CCC[C@H](O5)C)N2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44576167
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001729] Oxepanes

*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
NPT137 Cell Line L1210 Mus musculus Activity = 98 % PMID[1812209]
NPT2 Others Unspecified IC50 = 1000 nM PMID[14640525]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 1 ug/ml PMID[25435146]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 1 ug/ml PMID[25435146]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC = 2 ug/ml PMID[25435146]

☑ 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 NPC477518 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
0.8148 Intermediate Similarity NPC142761
0.7899 Intermediate Similarity NPC477519
0.7863 Intermediate Similarity NPC261730
0.7793 Intermediate Similarity NPC317377
0.7793 Intermediate Similarity NPC321485
0.7686 Intermediate Similarity NPC469389
0.7686 Intermediate Similarity NPC472737
0.7686 Intermediate Similarity NPC469388
0.7671 Intermediate Similarity NPC322372
0.7671 Intermediate Similarity NPC327517
0.7671 Intermediate Similarity NPC319334
0.7586 Intermediate Similarity NPC472736
0.6752 Remote Similarity NPC322966
0.6581 Remote Similarity NPC316244
0.6552 Remote Similarity NPC277918
0.6504 Remote Similarity NPC47076
0.6504 Remote Similarity NPC134504
0.6454 Remote Similarity NPC311244
0.6454 Remote Similarity NPC198644
0.6454 Remote Similarity NPC324722
0.6296 Remote Similarity NPC222481
0.6296 Remote Similarity NPC470621
0.6222 Remote Similarity NPC259586
0.6159 Remote Similarity NPC477237
0.6142 Remote Similarity NPC220234
0.6116 Remote Similarity NPC304454
0.6107 Remote Similarity NPC10897
0.6107 Remote Similarity NPC325900
0.6071 Remote Similarity NPC477238
0.6031 Remote Similarity NPC62845
0.6031 Remote Similarity NPC322449
0.6031 Remote Similarity NPC92874
0.6031 Remote Similarity NPC189854
0.6031 Remote Similarity NPC166242
0.6015 Remote Similarity NPC67009
0.5985 Remote Similarity NPC241394
0.5968 Remote Similarity NPC476019
0.5959 Remote Similarity NPC313657
0.5957 Remote Similarity NPC315188
0.5954 Remote Similarity NPC314398
0.5954 Remote Similarity NPC239705
0.5954 Remote Similarity NPC314413
0.592 Remote Similarity NPC471098
0.592 Remote Similarity NPC173763
0.592 Remote Similarity NPC62263
0.5909 Remote Similarity NPC128303
0.5903 Remote Similarity NPC309525
0.5887 Remote Similarity NPC475801
0.5887 Remote Similarity NPC474593
0.5882 Remote Similarity NPC476875
0.5878 Remote Similarity NPC301148
0.5878 Remote Similarity NPC5864
0.5878 Remote Similarity NPC471258
0.5878 Remote Similarity NPC124554
0.584 Remote Similarity NPC474576
0.5833 Remote Similarity NPC470653
0.5833 Remote Similarity NPC470654
0.5833 Remote Similarity NPC470650
0.5804 Remote Similarity NPC471262
0.5789 Remote Similarity NPC124549
0.5789 Remote Similarity NPC323720
0.5752 Remote Similarity NPC473955
0.5746 Remote Similarity NPC471259
0.5746 Remote Similarity NPC471844
0.5734 Remote Similarity NPC160688
0.5726 Remote Similarity NPC168017
0.5714 Remote Similarity NPC216090
0.5714 Remote Similarity NPC198344
0.5704 Remote Similarity NPC471261
0.5694 Remote Similarity NPC94319
0.5685 Remote Similarity NPC471263
0.5676 Remote Similarity NPC469387
0.5669 Remote Similarity NPC315237
0.5664 Remote Similarity NPC470652
0.5662 Remote Similarity NPC171734
0.5659 Remote Similarity NPC476261
0.5659 Remote Similarity NPC25033
0.5659 Remote Similarity NPC470382
0.5659 Remote Similarity NPC119225
0.5659 Remote Similarity NPC471635
0.5658 Remote Similarity NPC477400
0.5655 Remote Similarity NPC325750
0.5655 Remote Similarity NPC473477
0.5649 Remote Similarity NPC475188
0.5639 Remote Similarity NPC227622
0.5635 Remote Similarity NPC178632
0.562 Remote Similarity NPC473994
0.5615 Remote Similarity NPC473597
0.5615 Remote Similarity NPC471843
0.5603 Remote Similarity NPC296043
0.56 Remote Similarity NPC120335

  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 NPC477518 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
0.672 Remote Similarity NPD6122 Discontinued
0.6716 Remote Similarity NPD8347 Approved
0.6716 Remote Similarity NPD8345 Approved
0.6716 Remote Similarity NPD8346 Approved
0.6667 Remote Similarity NPD4825 Clinical (unspecified phase)
0.6585 Remote Similarity NPD3715 Approved
0.6585 Remote Similarity NPD3714 Approved
0.6585 Remote Similarity NPD3713 Approved
0.6583 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6562 Remote Similarity NPD1829 Clinical (unspecified phase)
0.6562 Remote Similarity NPD1827 Clinical (unspecified phase)
0.6562 Remote Similarity NPD1828 Approved
0.6441 Remote Similarity NPD3176 Clinical (unspecified phase)
0.6308 Remote Similarity NPD6937 Approved
0.6288 Remote Similarity NPD8087 Discontinued
0.623 Remote Similarity NPD2682 Approved
0.6183 Remote Similarity NPD8175 Discontinued
0.6061 Remote Similarity NPD8307 Discontinued
0.6061 Remote Similarity NPD8140 Approved
0.5906 Remote Similarity NPD7841 Clinical (unspecified phase)
0.587 Remote Similarity NPD7915 Approved
0.587 Remote Similarity NPD7916 Approved
0.584 Remote Similarity NPD4261 Phase 1
0.5814 Remote Similarity NPD8038 Phase 2
0.5793 Remote Similarity NPD8041 Phase 2
0.575 Remote Similarity NPD2683 Discontinued
0.5746 Remote Similarity NPD1385 Discontinued
0.5714 Remote Similarity NPD4780 Clinical (unspecified phase)
0.5694 Remote Similarity NPD4827 Approved
0.5694 Remote Similarity NPD4826 Approved
0.5694 Remote Similarity NPD4828 Approved
0.5693 Remote Similarity NPD1805 Phase 2
0.5693 Remote Similarity NPD1804 Phase 2
0.5691 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5662 Remote Similarity NPD6693 Phase 3
0.5639 Remote Similarity NPD8082 Approved
0.5639 Remote Similarity NPD8085 Approved
0.5639 Remote Similarity NPD8139 Approved
0.5639 Remote Similarity NPD8084 Approved
0.5639 Remote Similarity NPD8083 Approved
0.5639 Remote Similarity NPD8086 Approved
0.5639 Remote Similarity NPD8138 Approved
0.563 Remote Similarity NPD1428 Phase 2
0.562 Remote Similarity NPD8306 Approved
0.562 Remote Similarity NPD8305 Approved
0.5614 Remote Similarity NPD2696 Approved
0.5614 Remote Similarity NPD2695 Approved
0.5614 Remote Similarity NPD2694 Approved
0.5614 Remote Similarity NPD2697 Approved
0.56 Remote Similarity NPD3177 Phase 3

  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