Structure

Physi-Chem Properties

Molecular Weight:  453.15
Volume:  398.015
LogP:  -1.098
LogD:  -0.473
LogS:  -1.399
# Rotatable Bonds:  4
TPSA:  194.26
# H-Bond Aceptor:  14
# H-Bond Donor:  5
# Rings:  5
# Heavy Atoms:  14

MedChem Properties

QED Drug-Likeness Score:  0.303
Synthetic Accessibility Score:  5.325
Fsp3:  0.667
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:  -6.353
MDCK Permeability:  2.62224657490151e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.995
Human Intestinal Absorption (HIA):  0.965
20% Bioavailability (F20%):  0.233
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.324
Plasma Protein Binding (PPB):  25.45412826538086%
Volume Distribution (VD):  0.803
Pgp-substrate:  70.35569763183594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.9
CYP2C19-inhibitor:  0.043
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.009
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.058
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.114

ADMET: Excretion

Clearance (CL):  3.527
Half-life (T1/2):  0.84

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.945
Drug-inuced Liver Injury (DILI):  0.988
AMES Toxicity:  0.085
Rat Oral Acute Toxicity:  0.219
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.126
Carcinogencity:  0.028
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.541

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

  Natural Product: NPC282458

Natural Product ID:  NPC282458
Common Name*:   GZBSICLBZYSADI-ZKKAIADESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GZBSICLBZYSADI-ZKKAIADESA-N
Standard InCHI:  InChI=1S/C18H23N5O9/c1-28-12-10-6(30-16(12)23-5-22-8-14(19)20-4-21-15(8)23)3-7-18(27,32-10)13(25)9(24)11(31-7)17(26)29-2/h4-7,9-13,16,24-25,27H,3H2,1-2H3,(H2,19,20,21)/t6-,7-,9-,10+,11+,12-,13-,16-,18-/m1/s1
SMILES:  CO[C@@H]1[C@@H]2[C@@H](C[C@@H]3[C@@]([C@@H]([C@@H]([C@@H](C(=O)OC)O3)O)O)(O)O2)O[C@H]1n1cnc2c(N)ncnc12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3109447
PubChem CID:   76313958
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002203] Glycosylamines

*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
NPO32887 Streptomyces sp. L-9-10 Species Streptomycetaceae Bacteria organic extract n.a. n.a. PMID[24533857]
NPO40215 Streptomyces sp. CB01388 Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[29469575]

☑ 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
NPT71 Cell Line HEK293 Homo sapiens IC50 = 43700.0 nM PMID[557205]
NPT180 Cell Line HCT-8 Homo sapiens EC50 > 25000.0 nM PMID[557206]
NPT2615 Cell Line HEK-293T Homo sapiens CC50 > 40000.0 nM PMID[557206]
NPT65 Cell Line HepG2 Homo sapiens CC50 > 40000.0 nM PMID[557206]
NPT2 Others Unspecified IC50 = 3200.0 nM PMID[557205]
NPT2 Others Unspecified Inhibition = 53.0 % PMID[557205]
NPT2 Others Unspecified Inhibition = 92.2 % PMID[557205]
NPT1022 Organism Cryptosporidium parvum Cryptosporidium parvum EC50 > 25000.0 nM PMID[557206]

☑ 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 NPC282458 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
1.0 High Similarity NPC78941
0.9819 High Similarity NPC24589
0.9274 High Similarity NPC5802
0.9222 High Similarity NPC157821
0.9218 High Similarity NPC276373
0.8276 Intermediate Similarity NPC290959
0.7857 Intermediate Similarity NPC309832
0.7857 Intermediate Similarity NPC219313
0.7798 Intermediate Similarity NPC189068
0.7738 Intermediate Similarity NPC107374
0.7738 Intermediate Similarity NPC156461
0.7738 Intermediate Similarity NPC21448
0.7711 Intermediate Similarity NPC317821
0.7692 Intermediate Similarity NPC164665
0.7654 Intermediate Similarity NPC325906
0.7647 Intermediate Similarity NPC269827
0.7619 Intermediate Similarity NPC229974
0.7598 Intermediate Similarity NPC324484
0.7586 Intermediate Similarity NPC302778
0.7586 Intermediate Similarity NPC212551
0.7543 Intermediate Similarity NPC174802
0.7542 Intermediate Similarity NPC323091
0.75 Intermediate Similarity NPC224076
0.75 Intermediate Similarity NPC313897
0.75 Intermediate Similarity NPC161659
0.75 Intermediate Similarity NPC209525
0.7486 Intermediate Similarity NPC164952
0.7486 Intermediate Similarity NPC130586
0.7471 Intermediate Similarity NPC85689
0.7471 Intermediate Similarity NPC185991
0.7471 Intermediate Similarity NPC211025
0.7458 Intermediate Similarity NPC226245
0.7458 Intermediate Similarity NPC239737
0.7429 Intermediate Similarity NPC472816
0.7429 Intermediate Similarity NPC321814
0.7412 Intermediate Similarity NPC314152
0.7371 Intermediate Similarity NPC161224
0.736 Intermediate Similarity NPC316618
0.7356 Intermediate Similarity NPC136349
0.7337 Intermediate Similarity NPC129756
0.7314 Intermediate Similarity NPC150853
0.7299 Intermediate Similarity NPC121222
0.7232 Intermediate Similarity NPC207633
0.7232 Intermediate Similarity NPC328479
0.7222 Intermediate Similarity NPC195140
0.7219 Intermediate Similarity NPC326529
0.7181 Intermediate Similarity NPC324198
0.7181 Intermediate Similarity NPC319100
0.7113 Intermediate Similarity NPC313514
0.7097 Intermediate Similarity NPC326082
0.709 Intermediate Similarity NPC189261
0.7076 Intermediate Similarity NPC33996
0.7072 Intermediate Similarity NPC311197
0.7072 Intermediate Similarity NPC313754
0.7072 Intermediate Similarity NPC54320
0.7017 Intermediate Similarity NPC52238
0.6978 Remote Similarity NPC93365
0.6959 Remote Similarity NPC320818
0.6898 Remote Similarity NPC261595
0.6862 Remote Similarity NPC321458
0.6862 Remote Similarity NPC324033
0.6758 Remote Similarity NPC321052
0.6477 Remote Similarity NPC61198
0.6467 Remote Similarity NPC326694
0.642 Remote Similarity NPC262926
0.6404 Remote Similarity NPC30326
0.6374 Remote Similarity NPC274384
0.6374 Remote Similarity NPC89147
0.6339 Remote Similarity NPC64705
0.6339 Remote Similarity NPC232408
0.6319 Remote Similarity NPC251233
0.6319 Remote Similarity NPC211820
0.6284 Remote Similarity NPC177169
0.6284 Remote Similarity NPC317746
0.6271 Remote Similarity NPC319221
0.6231 Remote Similarity NPC164845
0.623 Remote Similarity NPC318590
0.6228 Remote Similarity NPC21461
0.6218 Remote Similarity NPC14590
0.6215 Remote Similarity NPC324009
0.6209 Remote Similarity NPC186619
0.6193 Remote Similarity NPC246193
0.6175 Remote Similarity NPC315642
0.6175 Remote Similarity NPC74306
0.6087 Remote Similarity NPC160666
0.6073 Remote Similarity NPC472834
0.6071 Remote Similarity NPC250178
0.6042 Remote Similarity NPC472833
0.6041 Remote Similarity NPC33382
0.6031 Remote Similarity NPC18308
0.6031 Remote Similarity NPC472832
0.601 Remote Similarity NPC125659
0.601 Remote Similarity NPC168702
0.6009 Remote Similarity NPC158055
0.595 Remote Similarity NPC222174
0.5945 Remote Similarity NPC103388
0.5942 Remote Similarity NPC265111
0.5902 Remote Similarity NPC473585
0.5838 Remote Similarity NPC321393
0.5819 Remote Similarity NPC107160
0.5805 Remote Similarity NPC327579
0.5803 Remote Similarity NPC473646
0.5769 Remote Similarity NPC57279
0.5746 Remote Similarity NPC104011
0.5714 Remote Similarity NPC217656
0.5689 Remote Similarity NPC476564
0.5684 Remote Similarity NPC89139
0.568 Remote Similarity NPC150447
0.5642 Remote Similarity NPC248007
0.5633 Remote Similarity NPC324815
0.5628 Remote Similarity NPC313504
0.5602 Remote Similarity NPC174114
0.5602 Remote Similarity NPC87981

  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 NPC282458 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
0.8187 Intermediate Similarity NPD5684 Clinical (unspecified phase)
0.8187 Intermediate Similarity NPD5682 Phase 3
0.8187 Intermediate Similarity NPD5683 Clinical (unspecified phase)
0.7895 Intermediate Similarity NPD3107 Discontinued
0.7886 Intermediate Similarity NPD3083 Approved
0.7861 Intermediate Similarity NPD2646 Discontinued
0.7738 Intermediate Similarity NPD249 Approved
0.7738 Intermediate Similarity NPD250 Approved
0.7654 Intermediate Similarity NPD1777 Approved
0.7654 Intermediate Similarity NPD1776 Approved
0.7647 Intermediate Similarity NPD195 Approved
0.7647 Intermediate Similarity NPD186 Discovery
0.7586 Intermediate Similarity NPD1369 Phase 2
0.7557 Intermediate Similarity NPD2624 Phase 2
0.7556 Intermediate Similarity NPD7988 Suspended
0.7543 Intermediate Similarity NPD339 Approved
0.75 Intermediate Similarity NPD5666 Phase 2
0.75 Intermediate Similarity NPD169 Phase 2
0.7486 Intermediate Similarity NPD1750 Clinical (unspecified phase)
0.7486 Intermediate Similarity NPD338 Approved
0.7471 Intermediate Similarity NPD283 Approved
0.7418 Intermediate Similarity NPD2647 Phase 3
0.7412 Intermediate Similarity NPD185 Approved
0.7386 Intermediate Similarity NPD242 Approved
0.736 Intermediate Similarity NPD1732 Phase 3
0.7356 Intermediate Similarity NPD548 Clinical (unspecified phase)
0.7326 Intermediate Similarity NPD166 Approved
0.7294 Intermediate Similarity NPD193 Suspended
0.724 Intermediate Similarity NPD6417 Clinical (unspecified phase)
0.7216 Intermediate Similarity NPD3708 Phase 2
0.7181 Intermediate Similarity NPD4171 Clinical (unspecified phase)
0.7126 Intermediate Similarity NPD7158 Phase 1
0.7113 Intermediate Similarity NPD7138 Phase 2
0.7072 Intermediate Similarity NPD216 Approved
0.7072 Intermediate Similarity NPD220 Clinical (unspecified phase)
0.7072 Intermediate Similarity NPD217 Approved
0.7072 Intermediate Similarity NPD218 Approved
0.7072 Intermediate Similarity NPD219 Phase 3
0.6979 Remote Similarity NPD4716 Approved
0.6978 Remote Similarity NPD546 Clinical (unspecified phase)
0.6963 Remote Similarity NPD1412 Clinical (unspecified phase)
0.6943 Remote Similarity NPD4744 Clinical (unspecified phase)
0.6906 Remote Similarity NPD213 Clinical (unspecified phase)
0.6906 Remote Similarity NPD214 Approved
0.6898 Remote Similarity NPD247 Clinical (unspecified phase)
0.6864 Remote Similarity NPD248 Discontinued
0.68 Remote Similarity NPD3695 Approved
0.68 Remote Similarity NPD3696 Approved
0.678 Remote Similarity NPD4240 Approved
0.6754 Remote Similarity NPD8291 Clinical (unspecified phase)
0.6734 Remote Similarity NPD2632 Approved
0.6734 Remote Similarity NPD2631 Clinical (unspecified phase)
0.6734 Remote Similarity NPD2630 Approved
0.6701 Remote Similarity NPD1692 Approved
0.6681 Remote Similarity NPD8375 Approved
0.6623 Remote Similarity NPD8371 Clinical (unspecified phase)
0.6612 Remote Similarity NPD7842 Phase 2
0.6596 Remote Similarity NPD516 Clinical (unspecified phase)
0.657 Remote Similarity NPD9632 Phase 3
0.655 Remote Similarity NPD870 Clinical (unspecified phase)
0.6524 Remote Similarity NPD2965 Clinical (unspecified phase)
0.6517 Remote Similarity NPD549 Approved
0.6512 Remote Similarity NPD9633 Phase 3
0.6477 Remote Similarity NPD252 Clinical (unspecified phase)
0.6453 Remote Similarity NPD4054 Clinical (unspecified phase)
0.6415 Remote Similarity NPD2876 Phase 3
0.6415 Remote Similarity NPD2877 Clinical (unspecified phase)
0.6389 Remote Similarity NPD2902 Phase 2
0.6389 Remote Similarity NPD2903 Clinical (unspecified phase)
0.6355 Remote Similarity NPD2824 Phase 2
0.6338 Remote Similarity NPD7323 Phase 2
0.6337 Remote Similarity NPD9408 Phase 3
0.6316 Remote Similarity NPD4074 Clinical (unspecified phase)
0.6304 Remote Similarity NPD7531 Clinical (unspecified phase)
0.6298 Remote Similarity NPD1430 Approved
0.6298 Remote Similarity NPD1431 Approved
0.629 Remote Similarity NPD3085 Phase 1
0.6273 Remote Similarity NPD5080 Phase 2
0.6257 Remote Similarity NPD3086 Phase 3
0.6245 Remote Similarity NPD6023 Discontinued
0.6236 Remote Similarity NPD194 Clinical (unspecified phase)
0.6227 Remote Similarity NPD5079 Phase 2
0.6223 Remote Similarity NPD536 Clinical (unspecified phase)
0.6223 Remote Similarity NPD9605 Phase 3
0.6209 Remote Similarity NPD5665 Clinical (unspecified phase)
0.6175 Remote Similarity NPD582 Approved
0.6133 Remote Similarity NPD1808 Phase 1
0.6089 Remote Similarity NPD1046 Clinical (unspecified phase)
0.6075 Remote Similarity NPD1730 Discontinued
0.6053 Remote Similarity NPD231 Clinical (unspecified phase)
0.6026 Remote Similarity NPD8409 Suspended
0.6022 Remote Similarity NPD171 Discontinued
0.6022 Remote Similarity NPD1121 Approved
0.6022 Remote Similarity NPD1120 Approved
0.6009 Remote Similarity NPD6840 Approved
0.6 Remote Similarity NPD4459 Clinical (unspecified phase)
0.6 Remote Similarity NPD4495 Phase 1
0.6 Remote Similarity NPD4458 Phase 2
0.5913 Remote Similarity NPD1063 Phase 2
0.5892 Remote Similarity NPD8250 Phase 2
0.5889 Remote Similarity NPD282 Approved
0.5879 Remote Similarity NPD1119 Phase 2
0.5867 Remote Similarity NPD5321 Phase 3
0.586 Remote Similarity NPD2253 Discontinued
0.5854 Remote Similarity NPD8373 Clinical (unspecified phase)
0.5847 Remote Similarity NPD535 Approved
0.5838 Remote Similarity NPD9606 Approved
0.5833 Remote Similarity NPD353 Discontinued
0.5826 Remote Similarity NPD5486 Discontinued
0.5805 Remote Similarity NPD9607 Approved
0.5782 Remote Similarity NPD2152 Clinical (unspecified phase)
0.5765 Remote Similarity NPD5336 Phase 1
0.5765 Remote Similarity NPD5337 Phase 1
0.5747 Remote Similarity NPD5458 Discontinued
0.5738 Remote Similarity NPD1058 Discontinued
0.573 Remote Similarity NPD6112 Approved
0.5729 Remote Similarity NPD2593 Clinical (unspecified phase)
0.5727 Remote Similarity NPD4715 Clinical (unspecified phase)
0.5727 Remote Similarity NPD4713 Clinical (unspecified phase)
0.5727 Remote Similarity NPD4714 Approved
0.5727 Remote Similarity NPD34 Approved
0.5722 Remote Similarity NPD1127 Approved
0.5722 Remote Similarity NPD1128 Approved
0.5689 Remote Similarity NPD6763 Discontinued
0.5672 Remote Similarity NPD7502 Clinical (unspecified phase)
0.5665 Remote Similarity NPD9584 Phase 2
0.5652 Remote Similarity NPD209 Clinical (unspecified phase)
0.5642 Remote Similarity NPD9084 Phase 2
0.5633 Remote Similarity NPD8271 Discontinued
0.5611 Remote Similarity NPD281 Approved
0.5607 Remote Similarity NPD8329 Phase 3
0.5603 Remote Similarity NPD6381 Phase 2

  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