Structure

Physi-Chem Properties

Molecular Weight:  803.5
Volume:  837.033
LogP:  3.992
LogD:  2.231
LogS:  -3.945
# Rotatable Bonds:  9
TPSA:  191.96
# H-Bond Aceptor:  15
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.178
Synthetic Accessibility Score:  5.997
Fsp3:  0.786
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:  -5.236
MDCK Permeability:  1.7746106095728464e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.601
Human Intestinal Absorption (HIA):  0.531
20% Bioavailability (F20%):  0.616
30% Bioavailability (F30%):  0.795

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  92.34359741210938%
Volume Distribution (VD):  0.718
Pgp-substrate:  1.205627679824829%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.025
CYP2C19-inhibitor:  0.067
CYP2C19-substrate:  0.575
CYP2C9-inhibitor:  0.076
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.088
CYP2D6-substrate:  0.079
CYP3A4-inhibitor:  0.898
CYP3A4-substrate:  0.823

ADMET: Excretion

Clearance (CL):  4.321
Half-life (T1/2):  0.061

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.991
Drug-inuced Liver Injury (DILI):  0.977
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.015
Maximum Recommended Daily Dose:  0.138
Skin Sensitization:  0.03
Carcinogencity:  0.025
Eye Corrosion:  0.003
Eye Irritation:  0.004
Respiratory Toxicity:  0.057

Download Data

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

  Natural Product: NPC67009

Natural Product ID:  NPC67009
Common Name*:   Viequeamide A
IUPAC Name:   (3R,6S,9S,13S,16S,19S,22S)-3-[(2S)-butan-2-yl]-16-[(1R)-1-hydroxyethyl]-7,12,12,20-tetramethyl-13-pent-4-ynyl-6,9,19-tri(propan-2-yl)-4,14-dioxa-1,7,10,17,20-pentazabicyclo[20.3.0]pentacosane-2,5,8,11,15,18,21-heptone
Synonyms:   Viequeamide A
Standard InCHIKey:  WRHBDNJXUOKAGU-LVWABFHYSA-N
Standard InCHI:  InChI=1S/C42H69N5O10/c1-15-17-18-21-29-42(11,12)41(55)44-30(23(3)4)37(51)46(14)33(25(7)8)40(54)57-34(26(9)16-2)38(52)47-22-19-20-28(47)36(50)45(13)32(24(5)6)35(49)43-31(27(10)48)39(53)56-29/h1,23-34,48H,16-22H2,2-14H3,(H,43,49)(H,44,55)/t26-,27+,28-,29-,30-,31-,32-,33-,34+/m0/s1
SMILES:  C#CCCC[C@@H]1OC(=O)[C@@H](N=C(O)[C@H](C(C)C)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@H](OC(=O)[C@@H](N(C(=O)[C@@H](N=C(C1(C)C)O)C(C)C)C)C(C)C)[C@H](CC)C)[C@H](O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2146621
PubChem CID:   71449228
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO32644 rivularia sp. Species Rivulariaceae Bacteria n.a. n.a. n.a. PMID[22924493]
NPO32644 rivularia sp. Species Rivulariaceae Bacteria n.a. n.a. n.a. PMID[23607568]

☑ 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
NPT397 Cell Line NCI-H460 Homo sapiens LD50 = 60.0 nM PMID[561412]
NPT91 Cell Line KB Homo sapiens IC50 < 100000.0 nM PMID[561413]
NPT81 Cell Line A549 Homo sapiens IC50 < 100000.0 nM PMID[561413]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 < 100000.0 nM PMID[561413]

☑ 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 NPC67009 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
0.9495 High Similarity NPC124554
0.9495 High Similarity NPC301148
0.9495 High Similarity NPC5864
0.9118 High Similarity NPC124549
0.902 High Similarity NPC198344
0.9 High Similarity NPC220234
0.8396 Intermediate Similarity NPC323720
0.8333 Intermediate Similarity NPC171734
0.7864 Intermediate Similarity NPC62263
0.7864 Intermediate Similarity NPC173763
0.7864 Intermediate Similarity NPC471098
0.7767 Intermediate Similarity NPC474576
0.767 Intermediate Similarity NPC475801
0.767 Intermediate Similarity NPC474593
0.7431 Intermediate Similarity NPC475440
0.7407 Intermediate Similarity NPC134504
0.7407 Intermediate Similarity NPC47076
0.7358 Intermediate Similarity NPC315237
0.7345 Intermediate Similarity NPC475637
0.7238 Intermediate Similarity NPC322966
0.7103 Intermediate Similarity NPC476019
0.7087 Intermediate Similarity NPC472351
0.708 Intermediate Similarity NPC471097
0.708 Intermediate Similarity NPC475149
0.7034 Intermediate Similarity NPC476875
0.7 Intermediate Similarity NPC477145
0.7 Intermediate Similarity NPC473741
0.6937 Remote Similarity NPC473597
0.6935 Remote Similarity NPC477238
0.6917 Remote Similarity NPC63191
0.6917 Remote Similarity NPC471202
0.6903 Remote Similarity NPC13175
0.6903 Remote Similarity NPC475791
0.6893 Remote Similarity NPC246005
0.6814 Remote Similarity NPC475758
0.6796 Remote Similarity NPC476302
0.6796 Remote Similarity NPC23984
0.6789 Remote Similarity NPC477538
0.6774 Remote Similarity NPC477237
0.6768 Remote Similarity NPC178919
0.6768 Remote Similarity NPC263281
0.6738 Remote Similarity NPC129666
0.6731 Remote Similarity NPC53858
0.6731 Remote Similarity NPC84128
0.6724 Remote Similarity NPC476877
0.672 Remote Similarity NPC470652
0.6714 Remote Similarity NPC329761
0.6714 Remote Similarity NPC225648
0.67 Remote Similarity NPC86064
0.6699 Remote Similarity NPC476117
0.6699 Remote Similarity NPC476243
0.6699 Remote Similarity NPC476156
0.6699 Remote Similarity NPC476137
0.6641 Remote Similarity NPC470654
0.6641 Remote Similarity NPC470650
0.6641 Remote Similarity NPC470653
0.661 Remote Similarity NPC241394
0.661 Remote Similarity NPC476876
0.6602 Remote Similarity NPC478017
0.6602 Remote Similarity NPC315535
0.6602 Remote Similarity NPC315131
0.6602 Remote Similarity NPC31756
0.66 Remote Similarity NPC43219
0.6589 Remote Similarity NPC309525
0.6585 Remote Similarity NPC103391
0.6585 Remote Similarity NPC472536
0.6532 Remote Similarity NPC296043
0.6525 Remote Similarity NPC128303
0.6509 Remote Similarity NPC235078
0.6505 Remote Similarity NPC316242
0.648 Remote Similarity NPC329216
0.6479 Remote Similarity NPC145113
0.6479 Remote Similarity NPC138775
0.6465 Remote Similarity NPC478256
0.6454 Remote Similarity NPC5620
0.6422 Remote Similarity NPC477728
0.6406 Remote Similarity NPC315188
0.6406 Remote Similarity NPC160688
0.6396 Remote Similarity NPC477729
0.6391 Remote Similarity NPC313657
0.6389 Remote Similarity NPC227051
0.6364 Remote Similarity NPC470655
0.6364 Remote Similarity NPC29598
0.6364 Remote Similarity NPC212866
0.6364 Remote Similarity NPC470651
0.6343 Remote Similarity NPC120335
0.633 Remote Similarity NPC477539
0.6321 Remote Similarity NPC470783
0.6321 Remote Similarity NPC475542
0.6312 Remote Similarity NPC139326
0.6306 Remote Similarity NPC275715
0.6296 Remote Similarity NPC145748
0.6296 Remote Similarity NPC155670
0.6296 Remote Similarity NPC95478
0.6271 Remote Similarity NPC188785
0.6263 Remote Similarity NPC10716
0.6241 Remote Similarity NPC269398
0.6241 Remote Similarity NPC263493
0.623 Remote Similarity NPC207820
0.6204 Remote Similarity NPC477730
0.62 Remote Similarity NPC475808
0.62 Remote Similarity NPC474298
0.62 Remote Similarity NPC473985
0.62 Remote Similarity NPC474299
0.62 Remote Similarity NPC28348
0.6197 Remote Similarity NPC161069
0.6183 Remote Similarity NPC50520
0.6132 Remote Similarity NPC312315
0.6124 Remote Similarity NPC469899
0.6116 Remote Similarity NPC205176
0.6081 Remote Similarity NPC162104
0.6071 Remote Similarity NPC52533
0.6028 Remote Similarity NPC471264
0.6028 Remote Similarity NPC471265
0.6015 Remote Similarity NPC477518
0.6 Remote Similarity NPC476130
0.6 Remote Similarity NPC476324
0.5987 Remote Similarity NPC197743
0.5987 Remote Similarity NPC297145
0.5981 Remote Similarity NPC473984
0.5968 Remote Similarity NPC296143
0.5962 Remote Similarity NPC209156
0.5962 Remote Similarity NPC266888
0.5962 Remote Similarity NPC256312
0.5962 Remote Similarity NPC161774
0.5962 Remote Similarity NPC138435
0.5946 Remote Similarity NPC277918
0.5944 Remote Similarity NPC46098
0.5944 Remote Similarity NPC268841
0.5944 Remote Similarity NPC307357
0.5931 Remote Similarity NPC476978
0.5915 Remote Similarity NPC68865
0.5909 Remote Similarity NPC47135
0.5905 Remote Similarity NPC327272
0.589 Remote Similarity NPC209509
0.5888 Remote Similarity NPC233108
0.5878 Remote Similarity NPC471821
0.5878 Remote Similarity NPC240848
0.5878 Remote Similarity NPC471820
0.5874 Remote Similarity NPC178662
0.5874 Remote Similarity NPC470884
0.5874 Remote Similarity NPC476133
0.5874 Remote Similarity NPC92784
0.5874 Remote Similarity NPC98424
0.5865 Remote Similarity NPC273185
0.5865 Remote Similarity NPC141325
0.5862 Remote Similarity NPC956
0.585 Remote Similarity NPC314358
0.5849 Remote Similarity NPC470782
0.5839 Remote Similarity NPC2501
0.5833 Remote Similarity NPC239762
0.5833 Remote Similarity NPC163392
0.5812 Remote Similarity NPC38172
0.5782 Remote Similarity NPC313867
0.5782 Remote Similarity NPC316008
0.5769 Remote Similarity NPC196007
0.5769 Remote Similarity NPC214532
0.5769 Remote Similarity NPC76297
0.5762 Remote Similarity NPC314050
0.5762 Remote Similarity NPC315809
0.5753 Remote Similarity NPC176226
0.5739 Remote Similarity NPC193386
0.5736 Remote Similarity NPC469597
0.5724 Remote Similarity NPC476259
0.5724 Remote Similarity NPC122590
0.5714 Remote Similarity NPC477643
0.5714 Remote Similarity NPC477641
0.5714 Remote Similarity NPC314388
0.5714 Remote Similarity NPC320865
0.5714 Remote Similarity NPC315283
0.5674 Remote Similarity NPC120420
0.5673 Remote Similarity NPC476291
0.5673 Remote Similarity NPC476285
0.5673 Remote Similarity NPC477642
0.566 Remote Similarity NPC126186
0.5652 Remote Similarity NPC473495
0.5648 Remote Similarity NPC59867
0.5648 Remote Similarity NPC472594
0.5635 Remote Similarity NPC137453
0.5634 Remote Similarity NPC99864
0.562 Remote Similarity NPC474371
0.5619 Remote Similarity NPC470781
0.5613 Remote Similarity NPC316244
0.5608 Remote Similarity NPC52748

  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 NPC67009 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
0.7103 Intermediate Similarity NPD4780 Clinical (unspecified phase)
0.6952 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6636 Remote Similarity NPD7759 Phase 2
0.6636 Remote Similarity NPD7760 Phase 2
0.6636 Remote Similarity NPD4261 Phase 1
0.6602 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6602 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6579 Remote Similarity NPD8038 Phase 2
0.6579 Remote Similarity NPD3715 Approved
0.6579 Remote Similarity NPD3713 Approved
0.6579 Remote Similarity NPD3714 Approved
0.6549 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6514 Remote Similarity NPD3177 Phase 3
0.6476 Remote Similarity NPD7762 Phase 2
0.6476 Remote Similarity NPD7763 Phase 2
0.6371 Remote Similarity NPD8298 Phase 2
0.6364 Remote Similarity NPD7840 Approved
0.6303 Remote Similarity NPD6122 Discontinued
0.6262 Remote Similarity NPD2683 Discontinued
0.6053 Remote Similarity NPD2682 Approved
0.5972 Remote Similarity NPD5193 Discontinued
0.5938 Remote Similarity NPD7916 Approved
0.5938 Remote Similarity NPD7915 Approved
0.5909 Remote Similarity NPD7345 Approved
0.5887 Remote Similarity NPD6937 Approved
0.5877 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5865 Remote Similarity NPD7652 Discontinued
0.5862 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5833 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5825 Remote Similarity NPD2694 Approved
0.5825 Remote Similarity NPD2696 Approved
0.5825 Remote Similarity NPD2697 Approved
0.5825 Remote Similarity NPD2695 Approved
0.5818 Remote Similarity NPD1125 Discovery
0.5818 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5798 Remote Similarity NPD1784 Approved
0.5794 Remote Similarity NPD8305 Approved
0.5794 Remote Similarity NPD2689 Clinical (unspecified phase)
0.5794 Remote Similarity NPD8306 Approved
0.5763 Remote Similarity NPD8394 Approved
0.5752 Remote Similarity NPD5791 Phase 2
0.5728 Remote Similarity NPD620 Approved
0.5728 Remote Similarity NPD3724 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5701 Remote Similarity NPD1453 Phase 1
0.5694 Remote Similarity NPD8173 Phase 2
0.5694 Remote Similarity NPD8172 Phase 2
0.5688 Remote Similarity NPD4815 Discontinued
0.5656 Remote Similarity NPD5359 Clinical (unspecified phase)
0.5641 Remote Similarity NPD5792 Clinical (unspecified phase)
0.5635 Remote Similarity NPD8140 Approved
0.5634 Remote Similarity NPD8415 Approved
0.5625 Remote Similarity NPD4260 Discontinued

  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