Structure

Physi-Chem Properties

Molecular Weight:  501.22
Volume:  441.478
LogP:  -3.576
LogD:  -2.899
LogS:  -0.293
# Rotatable Bonds:  7
TPSA:  286.05
# H-Bond Aceptor:  16
# H-Bond Donor:  14
# Rings:  3
# Heavy Atoms:  16

MedChem Properties

QED Drug-Likeness Score:  0.154
Synthetic Accessibility Score:  5.092
Fsp3:  1.0
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:  -6.42
MDCK Permeability:  0.0003059351001866162
Pgp-inhibitor:  0.0
Pgp-substrate:  0.983
Human Intestinal Absorption (HIA):  0.999
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.282
Plasma Protein Binding (PPB):  11.781192779541016%
Volume Distribution (VD):  0.215
Pgp-substrate:  80.12342834472656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.004
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.066
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.002
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.068
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.016

ADMET: Excretion

Clearance (CL):  1.044
Half-life (T1/2):  0.899

ADMET: Toxicity

hERG Blockers:  0.458
Human Hepatotoxicity (H-HT):  0.19
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.114
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.0
Skin Sensitization:  0.248
Carcinogencity:  0.005
Eye Corrosion:  0.026
Eye Irritation:  0.012
Respiratory Toxicity:  0.055

Download Data

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

  Natural Product: NPC318258

Natural Product ID:  NPC318258
Common Name*:   Chitotriose
IUPAC Name:   (2R,3S,4R,5R,6S)-5-amino-6-[(2R,3S,4R,5R,6S)-5-amino-6-[(2R,3S,4R,5R)-5-amino-4,6-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy-4-hydroxy-2-(hydroxymethyl)oxan-3-yl]oxy-2-(hydroxymethyl)oxane-3,4-diol
Synonyms:  
Standard InCHIKey:  RQFQJYYMBWVMQG-NLJWRWSBSA-N
Standard InCHI:  InChI=1S/C18H35N3O13/c19-7-12(27)14(5(2-23)30-16(7)29)33-18-9(21)13(28)15(6(3-24)32-18)34-17-8(20)11(26)10(25)4(1-22)31-17/h4-18,22-29H,1-3,19-21H2/t4-,5-,6-,7-,8-,9-,10-,11-,12-,13-,14-,15-,16?,17+,18+/m1/s1
SMILES:  C(C1C(C(C(C(O1)OC2C(OC(C(C2O)N)OC3C(OC(C(C3O)N)O)CO)CO)N)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3337491
PubChem CID:   11060176
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

*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
NPO30560 Thalassiosira pseudonana Species Thalassiosiraceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]

☑ 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
NPT2 Others Unspecified Kd = 14000.0 nM PMID[493376]

☑ 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 NPC318258 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
0.878 High Similarity NPC123746
0.878 High Similarity NPC477060
0.878 High Similarity NPC314408
0.878 High Similarity NPC314007
0.878 High Similarity NPC43850
0.8571 High Similarity NPC176381
0.8571 High Similarity NPC195969
0.8488 Intermediate Similarity NPC315334
0.8434 Intermediate Similarity NPC313552
0.8356 Intermediate Similarity NPC291650
0.8356 Intermediate Similarity NPC322801
0.8356 Intermediate Similarity NPC129100
0.8354 Intermediate Similarity NPC316807
0.8333 Intermediate Similarity NPC470282
0.8333 Intermediate Similarity NPC214376
0.8272 Intermediate Similarity NPC315969
0.825 Intermediate Similarity NPC70574
0.8214 Intermediate Similarity NPC306838
0.8171 Intermediate Similarity NPC263058
0.8125 Intermediate Similarity NPC98750
0.809 Intermediate Similarity NPC330590
0.8049 Intermediate Similarity NPC271772
0.8049 Intermediate Similarity NPC36927
0.7935 Intermediate Similarity NPC315036
0.7805 Intermediate Similarity NPC100204
0.7805 Intermediate Similarity NPC83248
0.7738 Intermediate Similarity NPC165119
0.7711 Intermediate Similarity NPC471420
0.7558 Intermediate Similarity NPC125253
0.7558 Intermediate Similarity NPC253975
0.7558 Intermediate Similarity NPC192025
0.7553 Intermediate Similarity NPC56298
0.7553 Intermediate Similarity NPC471628
0.7471 Intermediate Similarity NPC83839
0.747 Intermediate Similarity NPC150557
0.7416 Intermediate Similarity NPC470284
0.7342 Intermediate Similarity NPC327486
0.7342 Intermediate Similarity NPC223174
0.7342 Intermediate Similarity NPC327753
0.7162 Intermediate Similarity NPC317023
0.7021 Intermediate Similarity NPC470283
0.6989 Remote Similarity NPC270005
0.6989 Remote Similarity NPC328646
0.6989 Remote Similarity NPC208537
0.697 Remote Similarity NPC221148
0.6941 Remote Similarity NPC314772
0.6941 Remote Similarity NPC314968
0.6939 Remote Similarity NPC42320
0.6939 Remote Similarity NPC188453
0.6931 Remote Similarity NPC317534
0.68 Remote Similarity NPC472025
0.6778 Remote Similarity NPC476523
0.6731 Remote Similarity NPC57436
0.6731 Remote Similarity NPC121479
0.6729 Remote Similarity NPC313813
0.6712 Remote Similarity NPC67660
0.6712 Remote Similarity NPC269166
0.6712 Remote Similarity NPC89145
0.6712 Remote Similarity NPC157514
0.6712 Remote Similarity NPC165198
0.6712 Remote Similarity NPC58629
0.6712 Remote Similarity NPC242073
0.6712 Remote Similarity NPC107914
0.6712 Remote Similarity NPC246558
0.6712 Remote Similarity NPC145112
0.6711 Remote Similarity NPC34877
0.6711 Remote Similarity NPC290179
0.6709 Remote Similarity NPC6848
0.6622 Remote Similarity NPC303727
0.6604 Remote Similarity NPC314306
0.6542 Remote Similarity NPC241597
0.6538 Remote Similarity NPC477750
0.6538 Remote Similarity NPC477755
0.6538 Remote Similarity NPC477762
0.6538 Remote Similarity NPC477753
0.6538 Remote Similarity NPC477763
0.6538 Remote Similarity NPC477757
0.6456 Remote Similarity NPC17455
0.6442 Remote Similarity NPC59589
0.6438 Remote Similarity NPC326533
0.6429 Remote Similarity NPC476694
0.6429 Remote Similarity NPC476696
0.6429 Remote Similarity NPC476695
0.642 Remote Similarity NPC315980
0.6386 Remote Similarity NPC250619
0.6386 Remote Similarity NPC67099
0.6353 Remote Similarity NPC474468
0.6289 Remote Similarity NPC475603
0.6289 Remote Similarity NPC61894
0.6267 Remote Similarity NPC130683
0.6267 Remote Similarity NPC323361
0.6265 Remote Similarity NPC471418
0.625 Remote Similarity NPC306462
0.625 Remote Similarity NPC2432
0.625 Remote Similarity NPC69669
0.625 Remote Similarity NPC22774
0.625 Remote Similarity NPC218150
0.625 Remote Similarity NPC150680
0.6235 Remote Similarity NPC53760
0.6235 Remote Similarity NPC52268
0.6234 Remote Similarity NPC8979
0.6234 Remote Similarity NPC148424
0.622 Remote Similarity NPC190418
0.622 Remote Similarity NPC471761
0.622 Remote Similarity NPC471760
0.622 Remote Similarity NPC76881
0.622 Remote Similarity NPC12040
0.6216 Remote Similarity NPC233726
0.6216 Remote Similarity NPC23134
0.6216 Remote Similarity NPC124963
0.6203 Remote Similarity NPC143326
0.619 Remote Similarity NPC268922
0.619 Remote Similarity NPC475918
0.6176 Remote Similarity NPC255175
0.6176 Remote Similarity NPC271207
0.6176 Remote Similarity NPC206711
0.6176 Remote Similarity NPC225978
0.6154 Remote Similarity NPC314413
0.6154 Remote Similarity NPC239705
0.6154 Remote Similarity NPC314398
0.6145 Remote Similarity NPC477752
0.6145 Remote Similarity NPC477756
0.6145 Remote Similarity NPC477751
0.6145 Remote Similarity NPC477764
0.6125 Remote Similarity NPC472026
0.6098 Remote Similarity NPC198341
0.6098 Remote Similarity NPC471780
0.6098 Remote Similarity NPC471892
0.6098 Remote Similarity NPC223386
0.6098 Remote Similarity NPC75435
0.6098 Remote Similarity NPC142290
0.6095 Remote Similarity NPC189854
0.6095 Remote Similarity NPC166242
0.6095 Remote Similarity NPC62845
0.6095 Remote Similarity NPC92874
0.6095 Remote Similarity NPC322449
0.6092 Remote Similarity NPC169085
0.6092 Remote Similarity NPC9763
0.6092 Remote Similarity NPC225748
0.6092 Remote Similarity NPC163812
0.6092 Remote Similarity NPC206823
0.6092 Remote Similarity NPC39266
0.6087 Remote Similarity NPC94319
0.6071 Remote Similarity NPC477761
0.6071 Remote Similarity NPC477754
0.6071 Remote Similarity NPC477758
0.6071 Remote Similarity NPC477760
0.6071 Remote Similarity NPC477759
0.6047 Remote Similarity NPC299603
0.6047 Remote Similarity NPC28959
0.6047 Remote Similarity NPC285014
0.6047 Remote Similarity NPC255535
0.6047 Remote Similarity NPC137554
0.6038 Remote Similarity NPC10897
0.6038 Remote Similarity NPC325900
0.6024 Remote Similarity NPC147292
0.6024 Remote Similarity NPC286851
0.6024 Remote Similarity NPC303798
0.6 Remote Similarity NPC50228
0.6 Remote Similarity NPC97736
0.5979 Remote Similarity NPC292345
0.5949 Remote Similarity NPC219040
0.5948 Remote Similarity NPC20035
0.5946 Remote Similarity NPC282143
0.5946 Remote Similarity NPC299781
0.5946 Remote Similarity NPC42503
0.5946 Remote Similarity NPC157193
0.593 Remote Similarity NPC241265
0.593 Remote Similarity NPC475694
0.593 Remote Similarity NPC285003
0.593 Remote Similarity NPC473710
0.593 Remote Similarity NPC211428
0.5913 Remote Similarity NPC305261
0.5889 Remote Similarity NPC477350
0.5882 Remote Similarity NPC189629
0.5875 Remote Similarity NPC143809
0.5875 Remote Similarity NPC76726
0.5875 Remote Similarity NPC290106
0.5875 Remote Similarity NPC193593
0.5867 Remote Similarity NPC323574
0.5862 Remote Similarity NPC474078
0.5859 Remote Similarity NPC209047
0.5859 Remote Similarity NPC74672
0.5859 Remote Similarity NPC43074
0.5859 Remote Similarity NPC242503
0.5859 Remote Similarity NPC139782
0.5833 Remote Similarity NPC77191
0.5833 Remote Similarity NPC69798
0.5833 Remote Similarity NPC116377
0.5833 Remote Similarity NPC101746
0.5833 Remote Similarity NPC473952
0.5824 Remote Similarity NPC476782
0.5824 Remote Similarity NPC216883
0.5824 Remote Similarity NPC476781
0.5824 Remote Similarity NPC476783
0.5811 Remote Similarity NPC14144
0.58 Remote Similarity NPC111567
0.58 Remote Similarity NPC473581
0.58 Remote Similarity NPC186840
0.58 Remote Similarity NPC473604

  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 NPC318258 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
0.8889 High Similarity NPD3200 Clinical (unspecified phase)
0.878 High Similarity NPD3208 Approved
0.878 High Similarity NPD3209 Approved
0.878 High Similarity NPD3202 Approved
0.878 High Similarity NPD3201 Approved
0.878 High Similarity NPD3207 Approved
0.878 High Similarity NPD3203 Approved
0.8571 High Similarity NPD5795 Approved
0.8571 High Similarity NPD5796 Clinical (unspecified phase)
0.8571 High Similarity NPD5798 Approved
0.8571 High Similarity NPD5794 Approved
0.8571 High Similarity NPD5797 Approved
0.8356 Intermediate Similarity NPD9031 Approved
0.8356 Intermediate Similarity NPD9032 Approved
0.8356 Intermediate Similarity NPD9030 Approved
0.8356 Intermediate Similarity NPD9033 Approved
0.8333 Intermediate Similarity NPD2698 Approved
0.809 Intermediate Similarity NPD5377 Approved
0.809 Intermediate Similarity NPD5381 Approved
0.809 Intermediate Similarity NPD5378 Approved
0.7949 Intermediate Similarity NPD67 Phase 2
0.7949 Intermediate Similarity NPD9034 Approved
0.7802 Intermediate Similarity NPD6428 Approved
0.7717 Intermediate Similarity NPD4282 Approved
0.7553 Intermediate Similarity NPD4837 Approved
0.7553 Intermediate Similarity NPD4835 Approved
0.7553 Intermediate Similarity NPD4836 Approved
0.7553 Intermediate Similarity NPD4838 Approved
0.7347 Intermediate Similarity NPD5376 Approved
0.7342 Intermediate Similarity NPD9445 Approved
0.732 Intermediate Similarity NPD8045 Clinical (unspecified phase)
0.7158 Intermediate Similarity NPD881 Approved
0.7143 Intermediate Similarity NPD3716 Discontinued
0.7041 Intermediate Similarity NPD7141 Clinical (unspecified phase)
0.7041 Intermediate Similarity NPD7140 Approved
0.7041 Intermediate Similarity NPD7139 Approved
0.6974 Remote Similarity NPD6123 Approved
0.697 Remote Similarity NPD1450 Approved
0.697 Remote Similarity NPD1449 Approved
0.6961 Remote Similarity NPD6941 Approved
0.6941 Remote Similarity NPD9434 Approved
0.6941 Remote Similarity NPD9435 Approved
0.69 Remote Similarity NPD2700 Approved
0.6739 Remote Similarity NPD4759 Clinical (unspecified phase)
0.6737 Remote Similarity NPD1446 Phase 3
0.6737 Remote Similarity NPD1447 Phase 3
0.6731 Remote Similarity NPD35 Approved
0.6731 Remote Similarity NPD8087 Discontinued
0.6731 Remote Similarity NPD4833 Approved
0.6712 Remote Similarity NPD891 Phase 3
0.6712 Remote Similarity NPD890 Clinical (unspecified phase)
0.6712 Remote Similarity NPD888 Phase 3
0.6712 Remote Similarity NPD892 Phase 3
0.6712 Remote Similarity NPD893 Approved
0.6667 Remote Similarity NPD2690 Discontinued
0.6636 Remote Similarity NPD8345 Approved
0.6636 Remote Similarity NPD8346 Approved
0.6636 Remote Similarity NPD8347 Approved
0.6604 Remote Similarity NPD6429 Approved
0.6604 Remote Similarity NPD6430 Approved
0.6575 Remote Similarity NPD2269 Approved
0.6566 Remote Similarity NPD2255 Approved
0.6542 Remote Similarity NPD3731 Phase 3
0.6438 Remote Similarity NPD904 Phase 3
0.6438 Remote Similarity NPD905 Approved
0.6437 Remote Similarity NPD372 Clinical (unspecified phase)
0.6422 Remote Similarity NPD4832 Approved
0.6422 Remote Similarity NPD4830 Approved
0.6422 Remote Similarity NPD4831 Approved
0.64 Remote Similarity NPD7346 Approved
0.633 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6286 Remote Similarity NPD8307 Discontinued
0.6279 Remote Similarity NPD389 Phase 3
0.6267 Remote Similarity NPD894 Approved
0.6267 Remote Similarity NPD887 Approved
0.6267 Remote Similarity NPD889 Approved
0.6267 Remote Similarity NPD895 Approved
0.625 Remote Similarity NPD9026 Phase 2
0.625 Remote Similarity NPD9028 Phase 2
0.625 Remote Similarity NPD9029 Phase 3
0.625 Remote Similarity NPD9027 Phase 3
0.6237 Remote Similarity NPD361 Discontinued
0.6228 Remote Similarity NPD6436 Phase 3
0.6132 Remote Similarity NPD8140 Approved
0.6098 Remote Similarity NPD1457 Discontinued
0.6087 Remote Similarity NPD4827 Approved
0.6087 Remote Similarity NPD4826 Approved
0.6087 Remote Similarity NPD4828 Approved
0.6075 Remote Similarity NPD8174 Phase 2
0.6 Remote Similarity NPD9240 Approved
0.6 Remote Similarity NPD9239 Approved
0.6 Remote Similarity NPD9455 Approved
0.5979 Remote Similarity NPD618 Clinical (unspecified phase)
0.5977 Remote Similarity NPD6704 Discontinued
0.5926 Remote Similarity NPD393 Approved
0.5859 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5851 Remote Similarity NPD882 Phase 2
0.5851 Remote Similarity NPD883 Phase 2
0.5849 Remote Similarity NPD8275 Approved
0.5849 Remote Similarity NPD1407 Approved
0.5849 Remote Similarity NPD8276 Approved
0.5755 Remote Similarity NPD8138 Approved
0.5755 Remote Similarity NPD8084 Approved
0.5755 Remote Similarity NPD8083 Approved
0.5755 Remote Similarity NPD8139 Approved
0.5755 Remote Similarity NPD8086 Approved
0.5755 Remote Similarity NPD8082 Approved
0.5755 Remote Similarity NPD8085 Approved
0.5753 Remote Similarity NPD9000 Phase 3
0.5753 Remote Similarity NPD8999 Phase 3
0.5753 Remote Similarity NPD8998 Phase 2
0.5753 Remote Similarity NPD8997 Approved
0.5753 Remote Similarity NPD8993 Phase 1
0.575 Remote Similarity NPD369 Approved
0.5741 Remote Similarity NPD8393 Approved
0.573 Remote Similarity NPD3181 Approved
0.5714 Remote Similarity NPD3215 Phase 1
0.5699 Remote Similarity NPD7329 Approved
0.5686 Remote Similarity NPD8394 Approved
0.5648 Remote Similarity NPD8081 Approved
0.5625 Remote Similarity NPD2267 Suspended
0.56 Remote Similarity NPD8966 Approved
0.56 Remote Similarity NPD8965 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