Structure of PDB 6iyb Chain A Binding Site BS02

Receptor Information
>6iyb Chain A (length=171) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRL
VTMQIWDTAGLERFQSGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFL
IQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAK
EAINVEQAFQTIARNALKQET
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain6iyb Chain A Residue 1302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6iyb Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting.
Resolution2.091 Å
Binding residue
(original residue number in PDB)		S17 G18 G20 K21 T22 S23 F33 S34 N35 Y37 T40 G66 N125 K126 D128 L129 S155 K157
Binding residue
(residue number reindexed from 1)		S11 G12 G14 K15 T16 S17 F27 S28 N29 Y31 T34 G60 N118 K119 D121 L122 S148 K150
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0031267 small GTPase binding
GO:1905394 retromer complex binding
Biological Process
GO:0000045 autophagosome assembly
GO:0006622 protein targeting to lysosome
GO:0006897 endocytosis
GO:0006914 autophagy
GO:0007174 epidermal growth factor catabolic process
GO:0008333 endosome to lysosome transport
GO:0009617 response to bacterium
GO:0015031 protein transport
GO:0016042 lipid catabolic process
GO:0019076 viral release from host cell
GO:0022615 protein to membrane docking
GO:0036466 synaptic vesicle recycling via endosome
GO:0042147 retrograde transport, endosome to Golgi
GO:0045022 early endosome to late endosome transport
GO:0045453 bone resorption
GO:0045732 positive regulation of protein catabolic process
GO:0046907 intracellular transport
GO:0048524 positive regulation of viral process
GO:0051650 establishment of vesicle localization
GO:0061724 lipophagy
GO:0090382 phagosome maturation
GO:0090383 phagosome acidification
GO:0090385 phagosome-lysosome fusion
GO:0098943 neurotransmitter receptor transport, postsynaptic endosome to lysosome
GO:0099003 vesicle-mediated transport in synapse
GO:0099638 endosome to plasma membrane protein transport
GO:1903542 negative regulation of exosomal secretion
GO:1903543 positive regulation of exosomal secretion
GO:1905366 negative regulation of intralumenal vesicle formation
Cellular Component
GO:0000421 autophagosome membrane
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005794 Golgi apparatus
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030667 secretory granule membrane
GO:0030670 phagocytic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0030904 retromer complex
GO:0031902 late endosome membrane
GO:0031966 mitochondrial membrane
GO:0033162 melanosome membrane
GO:0034045 phagophore assembly site membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0045335 phagocytic vesicle
GO:0070062 extracellular exosome
GO:0097208 alveolar lamellar body
GO:0098588 bounding membrane of organelle
GO:0098830 presynaptic endosome
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6iyb, PDBe:6iyb, PDBj:6iyb
PDBsum6iyb
PubMed30721249
UniProtP51149|RAB7A_HUMAN Ras-related protein Rab-7a (Gene Name=RAB7A)

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