Structure

Physi-Chem Properties

Molecular Weight:  749.53
Volume:  798.69
LogP:  3.773
LogD:  3.531
LogS:  -3.668
# Rotatable Bonds:  33
TPSA:  194.24
# H-Bond Aceptor:  13
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  13

MedChem Properties

QED Drug-Likeness Score:  0.039
Synthetic Accessibility Score:  4.659
Fsp3:  0.8
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:  -5.31
MDCK Permeability:  4.092314338777214e-05
Pgp-inhibitor:  0.991
Pgp-substrate:  0.978
Human Intestinal Absorption (HIA):  0.888
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.049
Plasma Protein Binding (PPB):  80.58113861083984%
Volume Distribution (VD):  0.61
Pgp-substrate:  5.050987243652344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.04
CYP2C19-inhibitor:  0.13
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.273
CYP2C9-substrate:  0.066
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.045
CYP3A4-inhibitor:  0.908
CYP3A4-substrate:  0.103

ADMET: Excretion

Clearance (CL):  5.033
Half-life (T1/2):  0.873

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.952
Drug-inuced Liver Injury (DILI):  0.566
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.014
Maximum Recommended Daily Dose:  0.871
Skin Sensitization:  0.725
Carcinogencity:  0.091
Eye Corrosion:  0.003
Eye Irritation:  0.006
Respiratory Toxicity:  0.726

Download Data

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

  Natural Product: NPC476876

Natural Product ID:  NPC476876
Common Name*:   Cavinafungin B
IUPAC Name:   (2S,4R)-1-[(2S,3R)-3-hydroxy-2-[[(Z)-octadec-9-enoyl]amino]butanoyl]-N-[(2S)-1-[[(2S)-4-hydroxy-1-oxo-1-[[(2S)-1-oxopropan-2-yl]amino]butan-2-yl]amino]-3-methyl-1-oxobutan-2-yl]-4-methylpyrrolidine-2-carboxamide
Synonyms:  
Standard InCHIKey:  CZLLOPRJUYUCQD-AFRNNPFGSA-N
Standard InCHI:  InChI=1S/C40H71N5O8/c1-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-34(49)43-36(31(6)48)40(53)45-26-29(4)25-33(45)38(51)44-35(28(2)3)39(52)42-32(23-24-46)37(50)41-30(5)27-47/h14-15,27-33,35-36,46,48H,7-13,16-26H2,1-6H3,(H,41,50)(H,42,52)(H,43,49)(H,44,51)/b15-14-/t29-,30+,31-,32+,33+,35+,36+/m1/s1
SMILES:  CCCCCCCC/C=C\CCCCCCCC(=O)N[C@@H]([C@@H](C)O)C(=O)N1C[C@@H](C[C@H]1C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCO)C(=O)N[C@@H](C)C=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   122177447
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000348] Peptides
            • [CHEMONTID:0004831] Oligopeptides

*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
NPO33627 Colispora cavincola Species Eukaryota n.a. n.a. n.a. PMID[25636062]

☑ 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
NPT820 Organism Clavispora lusitaniae Clavispora lusitaniae MIC = 2 ug/ml PMID[25636062]
NPT554 Organism Candida glabrata Candida glabrata MIC = 2 ug/ml PMID[25636062]
NPT186 Organism Candida tropicalis Candida tropicalis MIC = 0.5 ug/ml PMID[25636062]
NPT20 Organism Candida albicans Candida albicans MIC > 32 ug/ml PMID[25636062]
NPT20 Organism Candida albicans Candida albicans MIC = 2 ug/ml PMID[25636062]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii MIC = 2 ug/ml PMID[25636062]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC = 2 ug/ml PMID[25636062]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC > 32 ug/ml PMID[25636062]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC80 = 8 ug/ml PMID[25636062]

☑ 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 NPC476876 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
0.9794 High Similarity NPC476877
0.951 High Similarity NPC476875
0.8148 Intermediate Similarity NPC207820
0.7931 Intermediate Similarity NPC315188
0.7652 Intermediate Similarity NPC296043
0.7586 Intermediate Similarity NPC329216
0.7547 Intermediate Similarity NPC47076
0.7547 Intermediate Similarity NPC134504
0.75 Intermediate Similarity NPC171734
0.7407 Intermediate Similarity NPC475758
0.7402 Intermediate Similarity NPC287401
0.7339 Intermediate Similarity NPC13175
0.7339 Intermediate Similarity NPC475791
0.7333 Intermediate Similarity NPC160688
0.7273 Intermediate Similarity NPC188785
0.725 Intermediate Similarity NPC470652
0.7213 Intermediate Similarity NPC50520
0.7207 Intermediate Similarity NPC475149
0.7207 Intermediate Similarity NPC471097
0.7115 Intermediate Similarity NPC324506
0.7097 Intermediate Similarity NPC46427
0.7097 Intermediate Similarity NPC309525
0.7071 Intermediate Similarity NPC31756
0.7016 Intermediate Similarity NPC470650
0.7016 Intermediate Similarity NPC252878
0.7016 Intermediate Similarity NPC470654
0.7016 Intermediate Similarity NPC470653
0.7008 Intermediate Similarity NPC319766
0.7 Intermediate Similarity NPC476243
0.7 Intermediate Similarity NPC476137
0.7 Intermediate Similarity NPC476156
0.7 Intermediate Similarity NPC476117
0.6992 Remote Similarity NPC273185
0.6972 Remote Similarity NPC469739
0.696 Remote Similarity NPC6975
0.6935 Remote Similarity NPC202521
0.6931 Remote Similarity NPC470783
0.6931 Remote Similarity NPC476302
0.693 Remote Similarity NPC128303
0.6923 Remote Similarity NPC251122
0.6887 Remote Similarity NPC275715
0.687 Remote Similarity NPC241394
0.6855 Remote Similarity NPC476990
0.685 Remote Similarity NPC470655
0.685 Remote Similarity NPC470651
0.6846 Remote Similarity NPC130309
0.6833 Remote Similarity NPC103391
0.6833 Remote Similarity NPC472536
0.6822 Remote Similarity NPC120335
0.6786 Remote Similarity NPC220234
0.6762 Remote Similarity NPC477539
0.6726 Remote Similarity NPC233932
0.6716 Remote Similarity NPC471265
0.6716 Remote Similarity NPC471264
0.6699 Remote Similarity NPC184473
0.6692 Remote Similarity NPC248283
0.6667 Remote Similarity NPC475801
0.6667 Remote Similarity NPC474593
0.6638 Remote Similarity NPC205176
0.6636 Remote Similarity NPC38172
0.6619 Remote Similarity NPC314358
0.661 Remote Similarity NPC67009
0.6606 Remote Similarity NPC474576
0.66 Remote Similarity NPC470782
0.6594 Remote Similarity NPC476978
0.6587 Remote Similarity NPC200964
0.6547 Remote Similarity NPC316008
0.6547 Remote Similarity NPC313867
0.6545 Remote Similarity NPC62263
0.6545 Remote Similarity NPC173763
0.6545 Remote Similarity NPC471098
0.6515 Remote Similarity NPC300315
0.6509 Remote Similarity NPC477199
0.6503 Remote Similarity NPC162104
0.6496 Remote Similarity NPC476259
0.6476 Remote Similarity NPC474312
0.6475 Remote Similarity NPC314388
0.6475 Remote Similarity NPC315283
0.6466 Remote Similarity NPC255447
0.6466 Remote Similarity NPC5864
0.6466 Remote Similarity NPC301148
0.6466 Remote Similarity NPC124554
0.646 Remote Similarity NPC473597
0.6436 Remote Similarity NPC217095
0.6436 Remote Similarity NPC264417
0.6434 Remote Similarity NPC175726
0.6434 Remote Similarity NPC473491
0.6434 Remote Similarity NPC474082
0.6429 Remote Similarity NPC209509
0.6429 Remote Similarity NPC315266
0.6429 Remote Similarity NPC5620
0.6423 Remote Similarity NPC98424
0.6423 Remote Similarity NPC92784
0.6423 Remote Similarity NPC476133
0.6423 Remote Similarity NPC178662
0.6423 Remote Similarity NPC470884
0.6422 Remote Similarity NPC155230
0.6422 Remote Similarity NPC322966
0.641 Remote Similarity NPC198344
0.6408 Remote Similarity NPC312315
0.64 Remote Similarity NPC126186
0.6396 Remote Similarity NPC315237
0.6393 Remote Similarity NPC314550
0.6381 Remote Similarity NPC6902
0.6377 Remote Similarity NPC163392
0.6377 Remote Similarity NPC239762
0.637 Remote Similarity NPC477400
0.6364 Remote Similarity NPC2501
0.6357 Remote Similarity NPC52748
0.6356 Remote Similarity NPC323720
0.6356 Remote Similarity NPC124549
0.6355 Remote Similarity NPC475975
0.6348 Remote Similarity NPC475440
0.6341 Remote Similarity NPC63191
0.6341 Remote Similarity NPC471202
0.6331 Remote Similarity NPC469426
0.6331 Remote Similarity NPC269398
0.6331 Remote Similarity NPC469427
0.6331 Remote Similarity NPC263493
0.6324 Remote Similarity NPC141050
0.6319 Remote Similarity NPC7817
0.6319 Remote Similarity NPC475168
0.6312 Remote Similarity NPC322878
0.6306 Remote Similarity NPC477538
0.6303 Remote Similarity NPC475918
0.6299 Remote Similarity NPC470546
0.629 Remote Similarity NPC272166
0.6286 Remote Similarity NPC176226
0.6286 Remote Similarity NPC475542
0.6284 Remote Similarity NPC197743
0.6284 Remote Similarity NPC297145
0.627 Remote Similarity NPC17581
0.627 Remote Similarity NPC476155
0.627 Remote Similarity NPC470544
0.626 Remote Similarity NPC478024
0.6259 Remote Similarity NPC244509
0.6259 Remote Similarity NPC477401
0.6259 Remote Similarity NPC477399
0.625 Remote Similarity NPC129666
0.6242 Remote Similarity NPC469898
0.624 Remote Similarity NPC66007
0.6238 Remote Similarity NPC256312
0.6238 Remote Similarity NPC161774
0.6238 Remote Similarity NPC266888
0.6233 Remote Similarity NPC122590
0.6231 Remote Similarity NPC36254
0.6226 Remote Similarity NPC284456
0.6224 Remote Similarity NPC145113
0.622 Remote Similarity NPC470788
0.622 Remote Similarity NPC469899
0.622 Remote Similarity NPC470545
0.62 Remote Similarity NPC196007
0.62 Remote Similarity NPC97614
0.62 Remote Similarity NPC214532
0.62 Remote Similarity NPC76297
0.62 Remote Similarity NPC470781
0.6194 Remote Similarity NPC473322
0.619 Remote Similarity NPC470902
0.6181 Remote Similarity NPC471820
0.6181 Remote Similarity NPC240848
0.6181 Remote Similarity NPC471821
0.617 Remote Similarity NPC77905
0.617 Remote Similarity NPC142761
0.617 Remote Similarity NPC161069
0.6164 Remote Similarity NPC314050
0.6164 Remote Similarity NPC315809
0.6148 Remote Similarity NPC200589
0.6147 Remote Similarity NPC319913
0.6143 Remote Similarity NPC307357
0.6143 Remote Similarity NPC46098
0.6143 Remote Similarity NPC268841
0.6133 Remote Similarity NPC244336
0.6122 Remote Similarity NPC262166
0.6115 Remote Similarity NPC127741
0.6111 Remote Similarity NPC225648
0.6111 Remote Similarity NPC329761
0.6106 Remote Similarity NPC314500
0.6099 Remote Similarity NPC168113
0.6091 Remote Similarity NPC322672
0.609 Remote Similarity NPC328494
0.6078 Remote Similarity NPC209156
0.6075 Remote Similarity NPC82799
0.6071 Remote Similarity NPC39290
0.6071 Remote Similarity NPC315210
0.6071 Remote Similarity NPC315848
0.6071 Remote Similarity NPC159369
0.6056 Remote Similarity NPC139326
0.6056 Remote Similarity NPC197682
0.6053 Remote Similarity NPC73655
0.6042 Remote Similarity NPC262077
0.6036 Remote Similarity NPC473525
0.6036 Remote Similarity NPC473495
0.6033 Remote Similarity NPC475637
0.6018 Remote Similarity NPC17143
0.6018 Remote Similarity NPC47230
0.6016 Remote Similarity NPC239357
0.6 Remote Similarity NPC68865
0.6 Remote Similarity NPC138775
0.5987 Remote Similarity NPC469901
0.5984 Remote Similarity NPC271562

  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 NPC476876 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
0.7426 Intermediate Similarity NPD3723 Clinical (unspecified phase)
0.697 Remote Similarity NPD8173 Phase 2
0.697 Remote Similarity NPD8172 Phase 2
0.6916 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6667 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6642 Remote Similarity NPD7113 Clinical (unspecified phase)
0.6538 Remote Similarity NPD2683 Discontinued
0.6481 Remote Similarity NPD3177 Phase 3
0.6449 Remote Similarity NPD7760 Phase 2
0.6449 Remote Similarity NPD7759 Phase 2
0.6442 Remote Similarity NPD7763 Phase 2
0.6442 Remote Similarity NPD7762 Phase 2
0.6404 Remote Similarity NPD8038 Phase 2
0.6339 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6324 Remote Similarity NPD8416 Discontinued
0.6306 Remote Similarity NPD4261 Phase 1
0.629 Remote Similarity NPD1000 Clinical (unspecified phase)
0.6134 Remote Similarity NPD6122 Discontinued
0.6067 Remote Similarity NPD7118 Clinical (unspecified phase)
0.6045 Remote Similarity NPD2585 Clinical (unspecified phase)
0.6028 Remote Similarity NPD7728 Clinical (unspecified phase)
0.6 Remote Similarity NPD4782 Clinical (unspecified phase)
0.6 Remote Similarity NPD5339 Clinical (unspecified phase)
0.6 Remote Similarity NPD8323 Discontinued
0.5944 Remote Similarity NPD8076 Discontinued
0.594 Remote Similarity NPD2584 Suspended
0.594 Remote Similarity NPD8273 Phase 1
0.5929 Remote Similarity NPD8643 Discontinued
0.5854 Remote Similarity NPD6937 Approved
0.5854 Remote Similarity NPD2147 Approved
0.5839 Remote Similarity NPD7613 Discontinued
0.5827 Remote Similarity NPD8415 Approved
0.5797 Remote Similarity NPD4125 Approved
0.5794 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5794 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5778 Remote Similarity NPD7746 Phase 1
0.5778 Remote Similarity NPD7747 Phase 1
0.5769 Remote Similarity NPD7756 Clinical (unspecified phase)
0.5763 Remote Similarity NPD4228 Discovery
0.5753 Remote Similarity NPD6860 Clinical (unspecified phase)
0.575 Remote Similarity NPD8126 Clinical (unspecified phase)
0.575 Remote Similarity NPD8124 Phase 3
0.5745 Remote Similarity NPD4791 Clinical (unspecified phase)
0.5739 Remote Similarity NPD790 Approved
0.5725 Remote Similarity NPD3159 Discontinued
0.5714 Remote Similarity NPD3713 Approved
0.5714 Remote Similarity NPD6421 Discontinued
0.5714 Remote Similarity NPD3714 Approved
0.5714 Remote Similarity NPD3715 Approved
0.5714 Remote Similarity NPD6676 Phase 2
0.5714 Remote Similarity NPD3632 Clinical (unspecified phase)
0.5705 Remote Similarity NPD7892 Clinical (unspecified phase)
0.5704 Remote Similarity NPD5767 Discontinued
0.5703 Remote Similarity NPD1376 Discontinued
0.5692 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5692 Remote Similarity NPD6935 Phase 3
0.569 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5683 Remote Similarity NPD7979 Clinical (unspecified phase)
0.5682 Remote Similarity NPD2645 Approved
0.5674 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5673 Remote Similarity NPD266 Phase 3
0.5673 Remote Similarity NPD265 Phase 3
0.5636 Remote Similarity NPD1125 Discovery
0.5635 Remote Similarity NPD6413 Approved
0.563 Remote Similarity NPD3191 Approved
0.563 Remote Similarity NPD3190 Approved
0.563 Remote Similarity NPD8299 Approved
0.563 Remote Similarity NPD3189 Approved
0.563 Remote Similarity NPD8342 Approved
0.563 Remote Similarity NPD8341 Approved
0.563 Remote Similarity NPD8340 Approved
0.5625 Remote Similarity NPD6901 Phase 3
0.5621 Remote Similarity NPD8414 Discontinued
0.5612 Remote Similarity NPD3626 Phase 3
0.5612 Remote Similarity NPD4177 Approved
0.5612 Remote Similarity NPD4175 Approved
0.5603 Remote Similarity NPD2682 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