Structure of PDB 6r3v Chain B Binding Site BS01

Receptor Information
>6r3v Chain B (length=172) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAIRKKLVIVGDGACGKTCLLIVYVPTVFENYVADIEVDGKQVELALWDT
AGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNV
PIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECS
AKTKDGVREVFEMATRAALQAR
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain6r3v Chain B Residue 202 [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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PDB6r3v A GAP-GTPase-GDP-PiIntermediate Crystal Structure Analyzed by DFT Shows GTP Hydrolysis Involves Serial Proton Transfers.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		A15 G17 K18 T19 C20 K118 D120 L121 S160 A161 K162
Binding residue
(residue number reindexed from 1)		A14 G16 K17 T18 C19 K108 D110 L111 S150 A151 K152
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:0017022 myosin binding
GO:0019901 protein kinase binding
Biological Process
GO:0000902 cell morphogenesis
GO:0001764 neuron migration
GO:0001822 kidney development
GO:0001998 angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure
GO:0002363 alpha-beta T cell lineage commitment
GO:0003100 regulation of systemic arterial blood pressure by endothelin
GO:0003189 aortic valve formation
GO:0006357 regulation of transcription by RNA polymerase II
GO:0007010 cytoskeleton organization
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0007264 small GTPase-mediated signal transduction
GO:0007266 Rho protein signal transduction
GO:0007519 skeletal muscle tissue development
GO:0010812 negative regulation of cell-substrate adhesion
GO:0010975 regulation of neuron projection development
GO:0016477 cell migration
GO:0021762 substantia nigra development
GO:0021795 cerebral cortex cell migration
GO:0021861 forebrain radial glial cell differentiation
GO:0030036 actin cytoskeleton organization
GO:0030154 cell differentiation
GO:0030334 regulation of cell migration
GO:0030521 androgen receptor signaling pathway
GO:0031122 cytoplasmic microtubule organization
GO:0032467 positive regulation of cytokinesis
GO:0032956 regulation of actin cytoskeleton organization
GO:0033144 negative regulation of intracellular steroid hormone receptor signaling pathway
GO:0033688 regulation of osteoblast proliferation
GO:0034329 cell junction assembly
GO:0034446 substrate adhesion-dependent cell spreading
GO:0035385 Roundabout signaling pathway
GO:0036089 cleavage furrow formation
GO:0038027 apolipoprotein A-I-mediated signaling pathway
GO:0042476 odontogenesis
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0043149 stress fiber assembly
GO:0043297 apical junction assembly
GO:0043366 beta selection
GO:0043542 endothelial cell migration
GO:0043931 ossification involved in bone maturation
GO:0044319 wound healing, spreading of cells
GO:0045198 establishment of epithelial cell apical/basal polarity
GO:0045666 positive regulation of neuron differentiation
GO:0045792 negative regulation of cell size
GO:0046638 positive regulation of alpha-beta T cell differentiation
GO:0050919 negative chemotaxis
GO:0051301 cell division
GO:0051496 positive regulation of stress fiber assembly
GO:0051893 regulation of focal adhesion assembly
GO:0060071 Wnt signaling pathway, planar cell polarity pathway
GO:0060193 positive regulation of lipase activity
GO:0061430 bone trabecula morphogenesis
GO:0070507 regulation of microtubule cytoskeleton organization
GO:0071222 cellular response to lipopolysaccharide
GO:0071345 cellular response to cytokine stimulus
GO:0071526 semaphorin-plexin signaling pathway
GO:0071803 positive regulation of podosome assembly
GO:0071902 positive regulation of protein serine/threonine kinase activity
GO:0090051 negative regulation of cell migration involved in sprouting angiogenesis
GO:0090307 mitotic spindle assembly
GO:0090324 negative regulation of oxidative phosphorylation
GO:0097049 motor neuron apoptotic process
GO:0097498 endothelial tube lumen extension
GO:0099159 regulation of modification of postsynaptic structure
GO:1901224 positive regulation of non-canonical NF-kappaB signal transduction
GO:1902766 skeletal muscle satellite cell migration
GO:1903427 negative regulation of reactive oxygen species biosynthetic process
GO:1903673 mitotic cleavage furrow formation
GO:1904695 positive regulation of vascular associated smooth muscle contraction
GO:1904996 positive regulation of leukocyte adhesion to vascular endothelial cell
GO:1905274 regulation of modification of postsynaptic actin cytoskeleton
GO:1990869 cellular response to chemokine
GO:2000177 regulation of neural precursor cell proliferation
GO:2000406 positive regulation of T cell migration
GO:2000672 negative regulation of motor neuron apoptotic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0005938 cell cortex
GO:0009898 cytoplasmic side of plasma membrane
GO:0030027 lamellipodium
GO:0030054 cell junction
GO:0030425 dendrite
GO:0030496 midbody
GO:0030667 secretory granule membrane
GO:0031982 vesicle
GO:0032154 cleavage furrow
GO:0032587 ruffle membrane
GO:0042995 cell projection
GO:0043197 dendritic spine
GO:0043296 apical junction complex
GO:0070062 extracellular exosome
GO:0071944 cell periphery
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse
GO:0101003 ficolin-1-rich granule membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6r3v, PDBe:6r3v, PDBj:6r3v
PDBsum6r3v
PubMed31038818
UniProtP61586|RHOA_HUMAN Transforming protein RhoA (Gene Name=RHOA)

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