Structure of PDB 3ped Chain A Binding Site BS01
Receptor Information
>3ped Chain A (length=177) Species:
9606
(Homo sapiens) [
Search protein sequence
] [
Download receptor structure
] [
Download structure with residue number starting from 1
] [
View receptor structure
]
DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKM
YATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYP
GLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKEN
FIRFSKSLGLPENHIVFPVPIDQCIDG
Ligand information
Ligand ID
ZYF
InChI
InChI=1S/C37H53N5O12/c1-25(23-31(44)38-27-16-11-14-22-42(52)36(27)49)54-37(50)28(39-34(48)29-24-53-35(40-29)26-15-9-10-18-30(26)43)17-12-13-21-41(51)32(45)19-7-5-3-2-4-6-8-20-33(46)47/h7,9-10,15,18-19,25,27-29,43,51-52H,2-6,8,11-14,16-17,20-24H2,1H3,(H,38,44)(H,39,48)(H,46,47)/b19-7-/t25-,27-,28-,29-/m0/s1
InChIKey
DRNVRDPDTBNRNR-SFCJKLQFSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.7.0
C[C@@H](CC(=O)N[C@H]1CCCCN(C1=O)O)OC(=O)[C@H](CCCCN(C(=O)/C=C\CCCCCCCC(=O)O)O)NC(=O)[C@@H]2COC(=N2)c3ccccc3O
ACDLabs 12.01
O=C(NC(C(=O)OC(C)CC(=O)NC1C(=O)N(O)CCCC1)CCCCN(O)C(=O)\C=C/CCCCCCCC(=O)O)C2N=C(OC2)c3c(O)cccc3
CACTVS 3.370
C[CH](CC(=O)N[CH]1CCCCN(O)C1=O)OC(=O)[CH](CCCCN(O)C(=O)C=CCCCCCCCC(O)=O)NC(=O)[CH]2COC(=N2)c3ccccc3O
CACTVS 3.370
C[C@@H](CC(=O)N[C@H]1CCCCN(O)C1=O)OC(=O)[C@H](CCCCN(O)C(=O)\C=C/CCCCCCCC(O)=O)NC(=O)[C@@H]2COC(=N2)c3ccccc3O
OpenEye OEToolkits 1.7.0
CC(CC(=O)NC1CCCCN(C1=O)O)OC(=O)C(CCCCN(C(=O)C=CCCCCCCCC(=O)O)O)NC(=O)C2COC(=N2)c3ccccc3O
Formula
C37 H53 N5 O12
Name
ChEMBL
DrugBank
ZINC
ZINC000098209684
PDB chain
3ped Chain A Residue 200 [
Download ligand structure
] [
Download structure with residue number starting from 1
] [
View ligand structure
]
Receptor-Ligand Complex Structure
Global view
Local view
Structure summary
[
Spin on
] [
Spin off
] [
Reset
]
[
High quality
] [
Low quality
]
[
White background
] [
Black background
]
[
Spin on
] [
Spin off
] [
Reset
]
[
High quality
] [
Low quality
]
[
White background
] [
Black background
]
PDB
3ped
Siderocalin Recognitin of Carboxymycobactins: Interference by the immune system in intracellular iron acquisition by Mycobacteria tuberculosis
Resolution
2.3 Å
Binding residue
(original residue number in PDB)
Y52 T54 L70 W79 R81 F123 K125 Y132 F133 K134 Y138
Binding residue
(residue number reindexed from 1)
Y51 T53 L69 W78 R80 F122 K124 Y131 F132 K133 Y137
Annotation score
1
Enzymatic activity
Enzyme Commision number
?
Gene Ontology
Molecular Function
GO:0005506
iron ion binding
GO:0005515
protein binding
GO:0036094
small molecule binding
GO:0042802
identical protein binding
GO:0140315
iron ion sequestering activity
GO:1903981
enterobactin binding
Biological Process
GO:0006826
iron ion transport
GO:0006915
apoptotic process
GO:0015891
siderophore transport
GO:0042742
defense response to bacterium
GO:0045087
innate immune response
GO:0120162
positive regulation of cold-induced thermogenesis
Cellular Component
GO:0005576
extracellular region
GO:0005615
extracellular space
GO:0031410
cytoplasmic vesicle
GO:0035580
specific granule lumen
GO:0060205
cytoplasmic vesicle lumen
GO:0070062
extracellular exosome
View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB
RCSB:3ped
,
PDBe:3ped
,
PDBj:3ped
PDBsum
3ped
PubMed
UniProt
P80188
|NGAL_HUMAN Neutrophil gelatinase-associated lipocalin (Gene Name=LCN2)
[
Back to BioLiP
]