Structure of PDB 4ydh Chain B Binding Site BS01

Receptor Information
>4ydh Chain B (length=178) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEP
YTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPE
ITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLK
AVKYVECSALTQRGLKNVFDEAILAALE
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain4ydh Chain B Residue 201 [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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PDB4ydh The structure of FMNL2-Cdc42 yields insights into the mechanism of lamellipodia and filopodia formation.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		A13 G15 K16 T17 C18 Y32 T35 G60 Q116 D118 L119 A159
Binding residue
(residue number reindexed from 1)		A13 G15 K16 T17 C18 Y32 T35 G60 Q116 D118 L119 A159
Annotation score3
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:0019901 protein kinase binding
GO:0030742 GTP-dependent protein binding
GO:0031435 mitogen-activated protein kinase kinase kinase binding
GO:0031996 thioesterase binding
GO:0032427 GBD domain binding
GO:0034191 apolipoprotein A-I receptor binding
GO:0042802 identical protein binding
GO:0061630 ubiquitin protein ligase activity
Biological Process
GO:0002040 sprouting angiogenesis
GO:0003015 heart process
GO:0003161 cardiac conduction system development
GO:0003253 cardiac neural crest cell migration involved in outflow tract morphogenesis
GO:0006897 endocytosis
GO:0006911 phagocytosis, engulfment
GO:0007015 actin filament organization
GO:0007030 Golgi organization
GO:0007088 regulation of mitotic nuclear division
GO:0007097 nuclear migration
GO:0007163 establishment or maintenance of cell polarity
GO:0007229 integrin-mediated signaling pathway
GO:0007264 small GTPase-mediated signal transduction
GO:0007399 nervous system development
GO:0008104 protein localization
GO:0009653 anatomical structure morphogenesis
GO:0010591 regulation of lamellipodium assembly
GO:0010592 positive regulation of lamellipodium assembly
GO:0021762 substantia nigra development
GO:0030036 actin cytoskeleton organization
GO:0030154 cell differentiation
GO:0030225 macrophage differentiation
GO:0030307 positive regulation of cell growth
GO:0030335 positive regulation of cell migration
GO:0031274 positive regulation of pseudopodium assembly
GO:0031333 negative regulation of protein-containing complex assembly
GO:0032467 positive regulation of cytokinesis
GO:0032488 Cdc42 protein signal transduction
GO:0032956 regulation of actin cytoskeleton organization
GO:0034329 cell junction assembly
GO:0034332 adherens junction organization
GO:0035050 embryonic heart tube development
GO:0035088 establishment or maintenance of apical/basal cell polarity
GO:0036336 dendritic cell migration
GO:0038189 neuropilin signaling pathway
GO:0043410 positive regulation of MAPK cascade
GO:0043525 positive regulation of neuron apoptotic process
GO:0044788 modulation by host of viral process
GO:0045198 establishment of epithelial cell apical/basal polarity
GO:0045740 positive regulation of DNA replication
GO:0046330 positive regulation of JNK cascade
GO:0046847 filopodium assembly
GO:0048549 positive regulation of pinocytosis
GO:0048664 neuron fate determination
GO:0051130 positive regulation of cellular component organization
GO:0051489 regulation of filopodium assembly
GO:0051491 positive regulation of filopodium assembly
GO:0051492 regulation of stress fiber assembly
GO:0051496 positive regulation of stress fiber assembly
GO:0051647 nucleus localization
GO:0051649 establishment of localization in cell
GO:0051683 establishment of Golgi localization
GO:0051835 positive regulation of synapse structural plasticity
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051988 regulation of attachment of spindle microtubules to kinetochore
GO:0060047 heart contraction
GO:0060071 Wnt signaling pathway, planar cell polarity pathway
GO:0060501 positive regulation of epithelial cell proliferation involved in lung morphogenesis
GO:0060661 submandibular salivary gland formation
GO:0060997 dendritic spine morphogenesis
GO:0071346 cellular response to type II interferon
GO:0072384 organelle transport along microtubule
GO:0086101 endothelin receptor signaling pathway involved in heart process
GO:0090135 actin filament branching
GO:0090316 positive regulation of intracellular protein transport
GO:0099159 regulation of modification of postsynaptic structure
GO:0099175 regulation of postsynapse organization
GO:1900026 positive regulation of substrate adhesion-dependent cell spreading
Cellular Component
GO:0000139 Golgi membrane
GO:0000322 storage vacuole
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005813 centrosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0017119 Golgi transport complex
GO:0030141 secretory granule
GO:0030175 filopodium
GO:0030425 dendrite
GO:0030496 midbody
GO:0031252 cell leading edge
GO:0031256 leading edge membrane
GO:0032991 protein-containing complex
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043197 dendritic spine
GO:0045177 apical part of cell
GO:0045335 phagocytic vesicle
GO:0051233 spindle midzone
GO:0070062 extracellular exosome
GO:0071944 cell periphery
GO:0072686 mitotic spindle
GO:0098685 Schaffer collateral - CA1 synapse
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ydh, PDBe:4ydh, PDBj:4ydh
PDBsum4ydh
PubMed25963737
UniProtP60953|CDC42_HUMAN Cell division control protein 42 homolog (Gene Name=CDC42)

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