NPASS Compound

Natural Product: NPC505645

Natural Product ID	NPC505645
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	STK249708
IUPAC Name	(2~{R},3~{R},4~{S},5~{S},6~{R})-2-(aminomethyl)-6-[(1~{S},2~{R},3~{S},4~{S},6~{S})-4,6-diamino-3-[(2~{S},3~{R},4~{R},5~{S},6~{R})-4-amino-3,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-2-hydroxy-cyclohexoxy]tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 69 71 0 0 0 0 0 0 0 0999 V2000 5.8542 -1.2077 -2.5072 N 0 0 0 0 0 0 0 0 0 0 0 0 4.6733 -0.5662 -2.0137 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9811 0.3517 -0.8265 C 0 0 1 0 0 0 0 0 0 0 0 0 3.7949 0.9244 -0.4163 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3164 0.2878 0.7175 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0207 0.6363 1.0310 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1281 -0.3975 1.0896 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0858 -0.1809 0.0197 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1710 1.1496 -0.4413 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3253 -0.3761 0.4881 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1250 -0.4800 -0.6523 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1328 0.4844 -0.6546 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9615 1.2618 -1.7690 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9862 2.1042 -2.0799 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2672 3.1919 -1.0970 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6027 2.7842 0.1645 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2040 1.2821 -2.4326 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8029 0.3826 -3.4342 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5908 0.4999 -1.2004 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5765 -0.4944 -1.6509 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.4377 -0.2714 -0.6263 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2971 -1.5399 -1.2315 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4208 -1.7151 1.1856 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0026 -2.7426 0.2538 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.5058 -1.7176 2.3586 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4405 -0.5382 2.4229 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1698 0.6709 2.8758 N 0 0 0 0 0 0 0 0 0 0 0 0 4.2379 0.6433 1.8583 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6985 0.2668 3.0895 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5745 0.0250 1.6066 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7820 -1.0326 2.5244 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6577 -0.4756 0.2048 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3376 -1.8508 0.1046 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9160 -2.2188 -2.2991 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7238 -0.6903 -2.2233 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9300 -1.3286 -1.7578 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2456 0.0496 -2.8429 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6817 1.1129 -1.2190 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3224 -0.8129 0.5894 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6494 -1.3717 0.8559 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2631 -0.8062 -0.8778 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1002 1.7915 0.3173 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7062 0.4494 1.0880 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0146 1.0807 0.2670 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6922 2.6235 -3.0408 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1505 3.7653 -1.5003 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3965 3.8967 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1407 3.3006 0.8450 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0564 1.8893 -2.7541 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0723 0.7437 -3.9885 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1208 1.1295 -0.4737 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5443 -0.2327 -1.3829 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3948 -1.4293 -1.2199 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6685 -0.4839 0.4382 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5132 -1.9624 -0.8102 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4565 -1.9097 1.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6623 -3.5499 0.3077 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0330 -3.0379 0.4961 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1249 -2.6346 2.3370 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0597 -1.7173 3.3210 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1811 -0.8258 3.2300 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0610 0.4996 3.4253 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4415 1.2107 3.5568 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3506 1.7661 1.8423 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9568 0.9005 3.2758 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3669 0.8015 1.8252 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8802 -0.5888 3.4261 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7620 -0.4600 -0.0545 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5016 -2.3101 0.9605 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 14 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 19 21 1 0 21 22 1 0 10 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 26 27 1 0 5 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 32 3 1 0 26 7 1 0 21 12 1 0 1 34 1 0 1 35 1 0 2 36 1 0 2 37 1 0 3 38 1 6 5 39 1 6 7 40 1 6 8 41 1 6 9 42 1 0 10 43 1 1 12 44 1 1 14 45 1 6 15 46 1 0 15 47 1 0 16 48 1 0 17 49 1 6 18 50 1 0 19 51 1 1 20 52 1 0 20 53 1 0 21 54 1 1 22 55 1 0 23 56 1 1 24 57 1 0 24 58 1 0 25 59 1 0 25 60 1 0 26 61 1 1 27 62 1 0 27 63 1 0 28 64 1 1 29 65 1 0 30 66 1 6 31 67 1 0 32 68 1 6 33 69 1 0 M END

Standard InCHIKey	SBUJHOSQTJFQJX-KDYJTNCSSA-N
Standard InCHI	InChI=1S/C18H36N4O11/c19-2-6-10(25)12(27)13(28)18(30-6)33-16-5(21)1-4(20)15(14(16)29)32-17-11(26)8(22)9(24)7(3-23)31-17/h4-18,23-29H,1-3,19-22H2/t4-,5-,6+,7+,8+,9+,10-,11+,12-,13-,14+,15-,16-,17+,18+/m0/s1
SMILES	NC[C@H]1O[C@H](O[C@@H]2[C@H](O)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@@H](N)[C@H]3O)[C@@H](N)C[C@@H]2N)[C@@H](O)[C@@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	484.24	Volume:	434.894 ? Van der Waals volume.
Dense:	1.113	LogP:	-1.327 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.319 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.835 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	18.0
TPSA:	282.61 ? Topological Polar Surface Area.	H-Bond Acceptor:	15.0
H-Bond Donor:	15.0	Rings:	3.0
Heavy Atoms:	15.0

MedChem Properties

QED Drug-Likeness Score:	0.167	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.052	Fsp³:	1.0
MCE-18:	69.333 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.647	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.084 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.116	Promiscuous compounds:	0.002

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.25	MDCK Permeability:	-5.508
Pgp-inhibitor:	0.0	Pgp-substrate:	0.999
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.973
20% Bioavailability (F20%):	0.818	30% Bioavailability (F30%):	0.919
50% Bioavailability (F50%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.121
Plasma Protein Binding (PPB):	10.877%	Volume Distribution (VD):	-0.628
Fu:	88.924% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.108
OATP1B3 inhibitor:	0.36	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

0.943

Half-life (T1/2):

2.271

ADMET: Toxicity

hERG Blockers:	0.028	hERG Blockers (10um):	0.088
Human Hepatotoxicity (H-HT):	0.472	Drug-induced Liver Injury (DILI):	0.0
AMES Toxicity:	0.355	Rat Oral Acute Toxicity:	0.014
Maximum Recommended Daily Dose:	0.094	Skin Sensitization:	1.0
Carcinogencity:	0.019	Eye Corrosion:	0.003
Eye Irritation:	0.002	Respiratory Toxicity:	0.047
Drug-induced Neurotoxicity:	0.555	Ototoxicity:	1.0
Hematotoxicity:	0.372	Drug-induced Nephrotoxicity:	0.565
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.104
A549 Cytotoxicity:	0.037	Hek293 Cytotoxicity:	0.005
BCF:	-0.016 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	1.859 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.305 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.019 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO896	Streptomyces kanamyceticus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO61927	Streptomyces kanamyceticus ATCC 12853	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO49913	Streptomyces lividans TK24	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO58610	Streptomyces kanamyceticus 12-6	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO51616	Streptomyces kanamyceticus 1375	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO57787	Streptomyces kanamyceticus IFO 13414	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO61431	Streptomyces kanamyceticus INA K-13	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO57959	Streptomyces kanamyceticus ISP 1375	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO47418	Streptomyces kanamyceticus ISP 5500	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO44146	Streptomyces tendae TÃ¼ 901/S 2566	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO896	Streptomyces kanamyceticus	Species	Streptomycetaceae	Bacteria	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	Organism Name	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

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC505645 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	36802
0.1-0.2	11454
0.2-0.3	1511
0.3-0.4	78
0.4-0.5	6
0.5-0.6	1
0.6-0.7	3
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC43850
1.0	High Similarity	NPC485811
0.902	High Similarity	NPC477060
0.7091	Intermediate Similarity	NPC611754
0.65	Remote Similarity	NPC607776
0.6491	Remote Similarity	NPC314408
0.6176	Remote Similarity	NPC330590
0.5902	Remote Similarity	NPC605029

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC505645 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7951
0.1-0.2	1110
0.2-0.3	53
0.3-0.4	25
0.4-0.5	3
0.5-0.6	2
0.6-0.7	3
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD3203	Phase 4
0.902	High Similarity	NPD3201	Approved
0.7917	Intermediate Similarity	NPD3200	Clinical (unspecified phase)
0.6491	Remote Similarity	NPD3208	Phase 4
0.6491	Remote Similarity	NPD3209	Approved
0.6176	Remote Similarity	NPD5378	Phase 4
0.5968	Remote Similarity	NPD3207	Approved
0.5833	Remote Similarity	NPD5377	Approved

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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