Structure

Physi-Chem Properties

Molecular Weight:  597.27
Volume:  584.404
LogP:  1.864
LogD:  1.211
LogS:  -3.401
# Rotatable Bonds:  8
TPSA:  171.71
# H-Bond Aceptor:  12
# H-Bond Donor:  4
# Rings:  6
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.11
Synthetic Accessibility Score:  6.147
Fsp3:  0.613
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:  -5.412
MDCK Permeability:  9.145940566668287e-06
Pgp-inhibitor:  0.07
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.164
20% Bioavailability (F20%):  0.966
30% Bioavailability (F30%):  0.517

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.145
Plasma Protein Binding (PPB):  39.43375778198242%
Volume Distribution (VD):  0.691
Pgp-substrate:  50.72057342529297%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.069
CYP2C19-inhibitor:  0.078
CYP2C19-substrate:  0.236
CYP2C9-inhibitor:  0.71
CYP2C9-substrate:  0.043
CYP2D6-inhibitor:  0.139
CYP2D6-substrate:  0.035
CYP3A4-inhibitor:  0.841
CYP3A4-substrate:  0.71

ADMET: Excretion

Clearance (CL):  3.181
Half-life (T1/2):  0.815

ADMET: Toxicity

hERG Blockers:  0.599
Human Hepatotoxicity (H-HT):  0.924
Drug-inuced Liver Injury (DILI):  0.843
AMES Toxicity:  0.301
Rat Oral Acute Toxicity:  0.878
Maximum Recommended Daily Dose:  0.988
Skin Sensitization:  0.477
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.914

Download Data

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

  Natural Product: NPC176245

Natural Product ID:  NPC176245
Common Name*:   Munroniamide
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  USEFZMBCGFCDMO-PNBNEUEUSA-N
Standard InCHI:  InChI=1S/C31H39N3O9/c1-15-24-25(41-22(37)7-10-29(24,5)19-14-23(38)43-28(19,3)4)26(40-16(2)35)30(6)18(13-20-31(15,30)42-20)17-9-12-34(27(17)39)21(36)8-11-33-32/h7,9-10,18-20,24-26,33H,1,8,11-14,32H2,2-6H3/t18-,19-,20+,24+,25+,26-,29-,30+,31+/m0/s1
SMILES:  NNCCC(=O)N1CC=C(C1=O)[C@@H]1C[C@@H]2[C@]3([C@@]1(C)[C@@H](OC(=O)C)[C@@H]1OC(=O)C=C[C@@]([C@@H]1C3=C)(C)[C@H]1CC(=O)OC1(C)C)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2268776
PubChem CID:   76323175
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:0000347] Amino acids and derivatives
            • [CHEMONTID:0001878] Beta amino acids and derivatives

*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
NPO9173 Munronia henryi Species Meliaceae Eukaryota whole plants Wenshan, Yunnan Province, China 2012-Nov PMID[25798528]
NPO27626 Limonia acidissima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9173 Munronia henryi Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3216 Comactinia meridionalis Species Comatulidae 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
NPT785 Organism Pieris brassicae Pieris brassicae mortality = 10.0 % PMID[503987]
NPT785 Organism Pieris brassicae Pieris brassicae Activity = 27.6 % PMID[503987]

☑ 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 NPC176245 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
0.7647 Intermediate Similarity NPC476558
0.7639 Intermediate Similarity NPC4548
0.7582 Intermediate Similarity NPC246209
0.7361 Intermediate Similarity NPC470793
0.7279 Intermediate Similarity NPC143755
0.7237 Intermediate Similarity NPC470851
0.7211 Intermediate Similarity NPC472667
0.7059 Intermediate Similarity NPC470850
0.7027 Intermediate Similarity NPC159928
0.6776 Remote Similarity NPC310511
0.6711 Remote Similarity NPC90472
0.6689 Remote Similarity NPC470420
0.6688 Remote Similarity NPC175186
0.6646 Remote Similarity NPC471170
0.6582 Remote Similarity NPC104382
0.6582 Remote Similarity NPC475371
0.6582 Remote Similarity NPC231529
0.6558 Remote Similarity NPC470277
0.6543 Remote Similarity NPC243902
0.6536 Remote Similarity NPC475520
0.6536 Remote Similarity NPC312536
0.6536 Remote Similarity NPC469380
0.65 Remote Similarity NPC189393
0.65 Remote Similarity NPC90814
0.6494 Remote Similarity NPC151616
0.6486 Remote Similarity NPC471934
0.6486 Remote Similarity NPC469370
0.6474 Remote Similarity NPC473979
0.6474 Remote Similarity NPC129992
0.6471 Remote Similarity NPC475372
0.6471 Remote Similarity NPC473720
0.646 Remote Similarity NPC476111
0.6456 Remote Similarity NPC287423
0.6443 Remote Similarity NPC253906
0.6424 Remote Similarity NPC470120
0.6415 Remote Similarity NPC476957
0.641 Remote Similarity NPC257017
0.641 Remote Similarity NPC162009
0.6395 Remote Similarity NPC470975
0.6395 Remote Similarity NPC470979
0.6395 Remote Similarity NPC103088
0.6392 Remote Similarity NPC473635
0.6387 Remote Similarity NPC145182
0.6387 Remote Similarity NPC471126
0.6387 Remote Similarity NPC157252
0.6387 Remote Similarity NPC472004
0.6387 Remote Similarity NPC471128
0.6369 Remote Similarity NPC472399
0.6369 Remote Similarity NPC469352
0.6369 Remote Similarity NPC473802
0.6369 Remote Similarity NPC469382
0.6364 Remote Similarity NPC124676
0.6364 Remote Similarity NPC146280
0.6358 Remote Similarity NPC471933
0.6351 Remote Similarity NPC180744
0.6346 Remote Similarity NPC204731
0.6346 Remote Similarity NPC52839
0.634 Remote Similarity NPC477509
0.634 Remote Similarity NPC234858
0.634 Remote Similarity NPC106228
0.634 Remote Similarity NPC471127
0.634 Remote Similarity NPC138372
0.634 Remote Similarity NPC154363
0.6335 Remote Similarity NPC473838
0.6335 Remote Similarity NPC475389
0.6333 Remote Similarity NPC473040
0.6329 Remote Similarity NPC75856
0.6329 Remote Similarity NPC473919
0.6329 Remote Similarity NPC473709
0.6329 Remote Similarity NPC469379
0.6329 Remote Similarity NPC321197
0.6329 Remote Similarity NPC86346
0.6329 Remote Similarity NPC145238
0.6323 Remote Similarity NPC156745
0.6323 Remote Similarity NPC9674
0.6323 Remote Similarity NPC19028
0.6323 Remote Similarity NPC236918
0.6319 Remote Similarity NPC471234
0.6319 Remote Similarity NPC478072
0.6306 Remote Similarity NPC222688
0.6306 Remote Similarity NPC170538
0.6299 Remote Similarity NPC10721
0.6299 Remote Similarity NPC473656
0.6296 Remote Similarity NPC180902
0.6296 Remote Similarity NPC475139
0.6296 Remote Similarity NPC472769
0.6289 Remote Similarity NPC471939
0.6289 Remote Similarity NPC293112
0.6282 Remote Similarity NPC472759
0.6282 Remote Similarity NPC474585
0.6282 Remote Similarity NPC475885
0.6282 Remote Similarity NPC329080
0.6275 Remote Similarity NPC178289
0.6273 Remote Similarity NPC472770
0.6266 Remote Similarity NPC11895
0.6258 Remote Similarity NPC171905
0.6258 Remote Similarity NPC472397
0.6258 Remote Similarity NPC471125
0.6258 Remote Similarity NPC472758
0.625 Remote Similarity NPC471940
0.625 Remote Similarity NPC5153
0.625 Remote Similarity NPC48414
0.6242 Remote Similarity NPC472401
0.6226 Remote Similarity NPC81736
0.6226 Remote Similarity NPC8369
0.6226 Remote Similarity NPC172154
0.622 Remote Similarity NPC182266
0.622 Remote Similarity NPC100017
0.622 Remote Similarity NPC471136
0.622 Remote Similarity NPC473548
0.622 Remote Similarity NPC475154
0.622 Remote Similarity NPC471137
0.622 Remote Similarity NPC223356
0.622 Remote Similarity NPC475500
0.6218 Remote Similarity NPC471108
0.6218 Remote Similarity NPC5292
0.6218 Remote Similarity NPC470186
0.6218 Remote Similarity NPC5989
0.6218 Remote Similarity NPC22628
0.6218 Remote Similarity NPC5991
0.6218 Remote Similarity NPC255081
0.6218 Remote Similarity NPC275696
0.6211 Remote Similarity NPC476078
0.6211 Remote Similarity NPC236999
0.6211 Remote Similarity NPC476091
0.6211 Remote Similarity NPC473620
0.6209 Remote Similarity NPC473535
0.6209 Remote Similarity NPC472757
0.6203 Remote Similarity NPC19464
0.6194 Remote Similarity NPC475323
0.6194 Remote Similarity NPC284068
0.6194 Remote Similarity NPC469684
0.6188 Remote Similarity NPC470973
0.6184 Remote Similarity NPC469656
0.6184 Remote Similarity NPC469655
0.6184 Remote Similarity NPC474846
0.6176 Remote Similarity NPC471172
0.6173 Remote Similarity NPC162495
0.6169 Remote Similarity NPC43213
0.6169 Remote Similarity NPC472400
0.6169 Remote Similarity NPC216665
0.6164 Remote Similarity NPC469789
0.6159 Remote Similarity NPC88668
0.6154 Remote Similarity NPC153440
0.6149 Remote Similarity NPC42399
0.6149 Remote Similarity NPC280903
0.6145 Remote Similarity NPC130447
0.6145 Remote Similarity NPC68282
0.6144 Remote Similarity NPC222834
0.6144 Remote Similarity NPC475391
0.614 Remote Similarity NPC194854
0.614 Remote Similarity NPC48813
0.6135 Remote Similarity NPC475606
0.6135 Remote Similarity NPC475314
0.6135 Remote Similarity NPC477189
0.6135 Remote Similarity NPC251564
0.6133 Remote Similarity NPC474716
0.6129 Remote Similarity NPC196931
0.6129 Remote Similarity NPC266728
0.6129 Remote Similarity NPC49492
0.6129 Remote Similarity NPC190286
0.6125 Remote Similarity NPC469790
0.6121 Remote Similarity NPC476823
0.6118 Remote Similarity NPC63511
0.6115 Remote Similarity NPC35037
0.6115 Remote Similarity NPC475041
0.6111 Remote Similarity NPC478136
0.6111 Remote Similarity NPC270109
0.6107 Remote Similarity NPC477127
0.6105 Remote Similarity NPC475462
0.6105 Remote Similarity NPC16729
0.6104 Remote Similarity NPC477126
0.6104 Remote Similarity NPC474937
0.6101 Remote Similarity NPC269642
0.6101 Remote Similarity NPC23786
0.6101 Remote Similarity NPC470265
0.6098 Remote Similarity NPC473485
0.6098 Remote Similarity NPC34963
0.6098 Remote Similarity NPC474508
0.6098 Remote Similarity NPC93416
0.6098 Remote Similarity NPC471855
0.609 Remote Similarity NPC156252
0.6087 Remote Similarity NPC217901
0.6087 Remote Similarity NPC15095
0.6078 Remote Similarity NPC194619
0.6078 Remote Similarity NPC96739
0.6078 Remote Similarity NPC260786
0.6078 Remote Similarity NPC474871
0.6078 Remote Similarity NPC174471
0.6076 Remote Similarity NPC251226
0.6076 Remote Similarity NPC19336
0.6076 Remote Similarity NPC79579
0.6076 Remote Similarity NPC475003
0.6076 Remote Similarity NPC185876
0.6074 Remote Similarity NPC470880
0.6074 Remote Similarity NPC91
0.6074 Remote Similarity NPC35109
0.6067 Remote Similarity NPC470980
0.6065 Remote Similarity NPC474872
0.6065 Remote Similarity NPC238667

  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 NPC176245 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
0.6196 Remote Similarity NPD7260 Phase 2
0.6174 Remote Similarity NPD6008 Approved
0.6159 Remote Similarity NPD6845 Suspended
0.6038 Remote Similarity NPD6921 Approved
0.6026 Remote Similarity NPD5954 Clinical (unspecified phase)
0.5988 Remote Similarity NPD7507 Approved
0.5976 Remote Similarity NPD7319 Approved
0.5964 Remote Similarity NPD8338 Approved
0.5909 Remote Similarity NPD5955 Clinical (unspecified phase)
0.589 Remote Similarity NPD8273 Phase 1
0.5864 Remote Similarity NPD7604 Phase 2
0.5839 Remote Similarity NPD6908 Approved
0.5839 Remote Similarity NPD6909 Approved
0.5813 Remote Similarity NPD7516 Approved
0.5786 Remote Similarity NPD7115 Discovery
0.5758 Remote Similarity NPD7078 Approved
0.575 Remote Similarity NPD7327 Approved
0.575 Remote Similarity NPD7328 Approved
0.5742 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5732 Remote Similarity NPD7492 Approved
0.5732 Remote Similarity NPD8297 Approved
0.5697 Remote Similarity NPD6616 Approved
0.5679 Remote Similarity NPD6054 Approved
0.5679 Remote Similarity NPD6319 Approved
0.5669 Remote Similarity NPD6649 Approved
0.5669 Remote Similarity NPD6650 Approved
0.5633 Remote Similarity NPD6053 Discontinued
0.5629 Remote Similarity NPD8337 Approved
0.5629 Remote Similarity NPD7736 Approved
0.5629 Remote Similarity NPD6648 Approved
0.5629 Remote Similarity NPD8336 Approved
0.5614 Remote Similarity NPD8415 Approved
0.5613 Remote Similarity NPD7899 Clinical (unspecified phase)
0.561 Remote Similarity NPD6370 Approved
0.5607 Remote Similarity NPD6334 Approved
0.5607 Remote Similarity NPD6333 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