Structure

Physi-Chem Properties

Molecular Weight:  497.34
Volume:  528.974
LogP:  5.153
LogD:  4.125
LogS:  -4.051
# Rotatable Bonds:  18
TPSA:  110.21
# H-Bond Aceptor:  8
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.323
Synthetic Accessibility Score:  4.326
Fsp3:  0.852
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.045
MDCK Permeability:  2.4797218429739587e-05
Pgp-inhibitor:  0.982
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.131
30% Bioavailability (F30%):  0.93

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.086
Plasma Protein Binding (PPB):  95.09220886230469%
Volume Distribution (VD):  0.589
Pgp-substrate:  4.135329723358154%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.151
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.882
CYP2C9-inhibitor:  0.227
CYP2C9-substrate:  0.676
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.095
CYP3A4-inhibitor:  0.31
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  6.835
Half-life (T1/2):  0.31

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.951
Drug-inuced Liver Injury (DILI):  0.938
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.105
Skin Sensitization:  0.492
Carcinogencity:  0.094
Eye Corrosion:  0.045
Eye Irritation:  0.012
Respiratory Toxicity:  0.036

Download Data

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

  Natural Product: NPC476019

Natural Product ID:  NPC476019
Common Name*:   Tumonoic Acid I
IUPAC Name:   (2S,3S)-2-[(2R,3S)-2-[(2S)-1-[(2S,4S)-2,4-dimethyloctanoyl]pyrrolidine-2-carbonyl]oxy-3-methylpentanoyl]oxy-3-methylpentanoic acid
Synonyms:   Tumonoic Acid I
Standard InCHIKey:  LWUJNFXMOSWRGO-HXWZHSPTSA-N
Standard InCHI:  InChI=1S/C27H47NO7/c1-8-11-13-17(4)16-20(7)24(29)28-15-12-14-21(28)26(32)35-23(19(6)10-3)27(33)34-22(25(30)31)18(5)9-2/h17-23H,8-16H2,1-7H3,(H,30,31)/t17-,18-,19-,20-,21-,22-,23+/m0/s1
SMILES:  CCCCC(C)CC(C)C(=O)N1CCCC1C(=O)OC(C(C)CC)C(=O)OC(C(C)CC)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL521892
PubChem CID:   25058102
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] 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
NPO33134 blennothrix cantharidosmum Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[18698821]

☑ 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 2000.0 nM PMID[475976]

☑ 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 NPC476019 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
0.8652 High Similarity NPC322966
0.7857 Intermediate Similarity NPC220234
0.7822 Intermediate Similarity NPC323720
0.7789 Intermediate Similarity NPC471098
0.7789 Intermediate Similarity NPC62263
0.7789 Intermediate Similarity NPC173763
0.7684 Intermediate Similarity NPC474576
0.7614 Intermediate Similarity NPC473741
0.7614 Intermediate Similarity NPC477145
0.7579 Intermediate Similarity NPC475801
0.7579 Intermediate Similarity NPC474593
0.7451 Intermediate Similarity NPC124554
0.7451 Intermediate Similarity NPC301148
0.7451 Intermediate Similarity NPC5864
0.7356 Intermediate Similarity NPC178919
0.7356 Intermediate Similarity NPC263281
0.7308 Intermediate Similarity NPC124549
0.7212 Intermediate Similarity NPC198344
0.7184 Intermediate Similarity NPC188785
0.7103 Intermediate Similarity NPC67009
0.7103 Intermediate Similarity NPC171734
0.7097 Intermediate Similarity NPC246005
0.7075 Intermediate Similarity NPC471844
0.7033 Intermediate Similarity NPC233108
0.701 Intermediate Similarity NPC52533
0.699 Remote Similarity NPC475440
0.6977 Remote Similarity NPC10716
0.6952 Remote Similarity NPC471097
0.6952 Remote Similarity NPC475149
0.6897 Remote Similarity NPC212866
0.6897 Remote Similarity NPC29598
0.6814 Remote Similarity NPC39041
0.6814 Remote Similarity NPC241294
0.6814 Remote Similarity NPC202722
0.6814 Remote Similarity NPC471846
0.6814 Remote Similarity NPC471845
0.6762 Remote Similarity NPC13175
0.6762 Remote Similarity NPC475791
0.6759 Remote Similarity NPC475637
0.6703 Remote Similarity NPC327272
0.6702 Remote Similarity NPC216090
0.6701 Remote Similarity NPC277918
0.6667 Remote Similarity NPC475758
0.6635 Remote Similarity NPC471843
0.6635 Remote Similarity NPC134504
0.6635 Remote Similarity NPC47076
0.6574 Remote Similarity NPC265094
0.65 Remote Similarity NPC324506
0.6491 Remote Similarity NPC471202
0.6491 Remote Similarity NPC63191
0.6491 Remote Similarity NPC469597
0.6455 Remote Similarity NPC241394
0.6446 Remote Similarity NPC474371
0.6446 Remote Similarity NPC309525
0.6396 Remote Similarity NPC271562
0.6364 Remote Similarity NPC128303
0.6354 Remote Similarity NPC474702
0.633 Remote Similarity NPC233274
0.633 Remote Similarity NPC287638
0.633 Remote Similarity NPC194750
0.6321 Remote Similarity NPC473597
0.6316 Remote Similarity NPC474411
0.6316 Remote Similarity NPC474431
0.6311 Remote Similarity NPC477538
0.625 Remote Similarity NPC315237
0.625 Remote Similarity NPC160661
0.625 Remote Similarity NPC477238
0.6195 Remote Similarity NPC474099
0.619 Remote Similarity NPC120335
0.6167 Remote Similarity NPC11379
0.6154 Remote Similarity NPC47230
0.6154 Remote Similarity NPC322274
0.6154 Remote Similarity NPC17143
0.6122 Remote Similarity NPC470783
0.6121 Remote Similarity NPC314550
0.6106 Remote Similarity NPC137453
0.61 Remote Similarity NPC472351
0.6098 Remote Similarity NPC470653
0.6098 Remote Similarity NPC470654
0.6098 Remote Similarity NPC470650
0.6094 Remote Similarity NPC120420
0.6087 Remote Similarity NPC469603
0.6083 Remote Similarity NPC477237
0.6064 Remote Similarity NPC43219
0.6058 Remote Similarity NPC178632
0.6058 Remote Similarity NPC471821
0.6058 Remote Similarity NPC471820
0.6047 Remote Similarity NPC99864
0.6045 Remote Similarity NPC956
0.6042 Remote Similarity NPC330017
0.6034 Remote Similarity NPC476875
0.602 Remote Similarity NPC476117
0.602 Remote Similarity NPC476137
0.602 Remote Similarity NPC476156
0.602 Remote Similarity NPC476243
0.6019 Remote Similarity NPC160066
0.6017 Remote Similarity NPC103391
0.6017 Remote Similarity NPC472536
0.6 Remote Similarity NPC47135
0.6 Remote Similarity NPC287693
0.6 Remote Similarity NPC86064
0.6 Remote Similarity NPC235625
0.5984 Remote Similarity NPC160688
0.5984 Remote Similarity NPC23963
0.5978 Remote Similarity NPC15864
0.5968 Remote Similarity NPC477518
0.5962 Remote Similarity NPC203170
0.596 Remote Similarity NPC23984
0.596 Remote Similarity NPC476302
0.594 Remote Similarity NPC470884
0.594 Remote Similarity NPC178662
0.594 Remote Similarity NPC98424
0.594 Remote Similarity NPC476133
0.594 Remote Similarity NPC92784
0.5922 Remote Similarity NPC322672
0.5918 Remote Similarity NPC31756
0.5918 Remote Similarity NPC312315
0.5914 Remote Similarity NPC478256
0.5914 Remote Similarity NPC476285
0.5914 Remote Similarity NPC476291
0.5913 Remote Similarity NPC207820
0.5902 Remote Similarity NPC470652
0.59 Remote Similarity NPC84128
0.59 Remote Similarity NPC53858
0.5895 Remote Similarity NPC138435
0.5895 Remote Similarity NPC209156
0.5895 Remote Similarity NPC256312
0.5895 Remote Similarity NPC266888
0.5895 Remote Similarity NPC161774
0.5895 Remote Similarity NPC320221
0.5893 Remote Similarity NPC474244
0.5893 Remote Similarity NPC227622
0.5865 Remote Similarity NPC88943
0.5865 Remote Similarity NPC168017
0.5865 Remote Similarity NPC473525
0.5852 Remote Similarity NPC269398
0.5852 Remote Similarity NPC263493
0.5851 Remote Similarity NPC170963
0.5851 Remote Similarity NPC33267
0.5851 Remote Similarity NPC324165
0.5851 Remote Similarity NPC126366
0.5851 Remote Similarity NPC169976
0.5851 Remote Similarity NPC114640
0.5841 Remote Similarity NPC68001
0.5841 Remote Similarity NPC474827
0.5841 Remote Similarity NPC474828
0.5841 Remote Similarity NPC199831
0.5839 Remote Similarity NPC5620
0.5833 Remote Similarity NPC296043
0.5833 Remote Similarity NPC297145
0.5833 Remote Similarity NPC197743
0.5827 Remote Similarity NPC240848
0.5825 Remote Similarity NPC319913
0.5824 Remote Similarity NPC326651
0.5824 Remote Similarity NPC325117
0.5824 Remote Similarity NPC322319
0.5816 Remote Similarity NPC162104
0.581 Remote Similarity NPC292345
0.5806 Remote Similarity NPC82315
0.5806 Remote Similarity NPC273185
0.5798 Remote Similarity NPC193471
0.5798 Remote Similarity NPC309731
0.5798 Remote Similarity NPC130124
0.5797 Remote Similarity NPC262077
0.5795 Remote Similarity NPC470363
0.5789 Remote Similarity NPC474403
0.5789 Remote Similarity NPC141325
0.5789 Remote Similarity NPC64168
0.5789 Remote Similarity NPC469604
0.5785 Remote Similarity NPC28542
0.5785 Remote Similarity NPC329216
0.5784 Remote Similarity NPC320936
0.5781 Remote Similarity NPC25327
0.5773 Remote Similarity NPC476324
0.5773 Remote Similarity NPC476130
0.5763 Remote Similarity NPC316984
0.5763 Remote Similarity NPC30911
0.576 Remote Similarity NPC473477
0.5758 Remote Similarity NPC473984
0.5755 Remote Similarity NPC145113
0.5741 Remote Similarity NPC469998
0.5729 Remote Similarity NPC208657
0.5729 Remote Similarity NPC476248
0.5727 Remote Similarity NPC313821
0.5726 Remote Similarity NPC315188
0.5725 Remote Similarity NPC209509
0.5714 Remote Similarity NPC333075
0.5714 Remote Similarity NPC274499
0.5714 Remote Similarity NPC472594
0.5714 Remote Similarity NPC8488
0.5702 Remote Similarity NPC173690
0.5702 Remote Similarity NPC476877
0.5702 Remote Similarity NPC6271
0.5702 Remote Similarity NPC279833
0.5702 Remote Similarity NPC271115
0.5702 Remote Similarity NPC80439
0.5699 Remote Similarity NPC469925
0.5686 Remote Similarity NPC235078
0.5684 Remote Similarity NPC196007
0.5684 Remote Similarity NPC76297

  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 NPC476019 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
0.7576 Intermediate Similarity NPD3715 Approved
0.7576 Intermediate Similarity NPD3714 Approved
0.7576 Intermediate Similarity NPD3713 Approved
0.697 Remote Similarity NPD2682 Approved
0.6897 Remote Similarity NPD7840 Approved
0.6818 Remote Similarity NPD2220 Clinical (unspecified phase)
0.68 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6633 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6495 Remote Similarity NPD882 Phase 2
0.6495 Remote Similarity NPD883 Phase 2
0.6444 Remote Similarity NPD2694 Approved
0.6444 Remote Similarity NPD2697 Approved
0.6444 Remote Similarity NPD9649 Approved
0.6444 Remote Similarity NPD2695 Approved
0.6444 Remote Similarity NPD2696 Approved
0.6421 Remote Similarity NPD617 Approved
0.6293 Remote Similarity NPD7915 Approved
0.6293 Remote Similarity NPD7916 Approved
0.625 Remote Similarity NPD8140 Approved
0.6154 Remote Similarity NPD4261 Phase 1
0.6139 Remote Similarity NPD7759 Phase 2
0.6139 Remote Similarity NPD7760 Phase 2
0.6122 Remote Similarity NPD7762 Phase 2
0.6122 Remote Similarity NPD7763 Phase 2
0.6106 Remote Similarity NPD8307 Discontinued
0.6078 Remote Similarity NPD3176 Clinical (unspecified phase)
0.6071 Remote Similarity NPD4281 Clinical (unspecified phase)
0.6047 Remote Similarity NPD8415 Approved
0.6045 Remote Similarity NPD5193 Discontinued
0.6 Remote Similarity NPD7345 Approved
0.6 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5982 Remote Similarity NPD8275 Approved
0.5982 Remote Similarity NPD6122 Discontinued
0.5982 Remote Similarity NPD8276 Approved
0.5979 Remote Similarity NPD8144 Approved
0.5979 Remote Similarity NPD8143 Approved
0.5978 Remote Similarity NPD620 Approved
0.5962 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5926 Remote Similarity NPD7841 Clinical (unspecified phase)
0.5914 Remote Similarity NPD3725 Approved
0.5914 Remote Similarity NPD3726 Approved
0.59 Remote Similarity NPD1125 Discovery
0.59 Remote Similarity NPD2683 Discontinued
0.5893 Remote Similarity NPD8301 Approved
0.5893 Remote Similarity NPD8082 Approved
0.5893 Remote Similarity NPD8085 Approved
0.5893 Remote Similarity NPD8083 Approved
0.5893 Remote Similarity NPD8300 Approved
0.5893 Remote Similarity NPD8084 Approved
0.5893 Remote Similarity NPD8139 Approved
0.5893 Remote Similarity NPD8086 Approved
0.5893 Remote Similarity NPD8138 Approved
0.5877 Remote Similarity NPD8393 Approved
0.5818 Remote Similarity NPD8038 Phase 2
0.5812 Remote Similarity NPD8087 Discontinued
0.581 Remote Similarity NPD618 Clinical (unspecified phase)
0.58 Remote Similarity NPD612 Discontinued
0.5798 Remote Similarity NPD1376 Discontinued
0.5794 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5789 Remote Similarity NPD8081 Approved
0.5773 Remote Similarity NPD11 Approved
0.5773 Remote Similarity NPD376 Approved
0.5773 Remote Similarity NPD1453 Phase 1
0.5772 Remote Similarity NPD8347 Approved
0.5772 Remote Similarity NPD8346 Approved
0.5772 Remote Similarity NPD8345 Approved
0.5763 Remote Similarity NPD2204 Approved
0.5727 Remote Similarity NPD3190 Approved
0.5727 Remote Similarity NPD3191 Approved
0.5727 Remote Similarity NPD3189 Approved
0.5726 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2689 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3177 Phase 3
0.569 Remote Similarity NPD6937 Approved
0.5662 Remote Similarity NPD8384 Approved
0.5625 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6704 Discontinued
0.5603 Remote Similarity NPD6920 Discontinued
0.5603 Remote Similarity NPD1385 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