Structure of PDB 7r04 Chain A Binding Site BS01

Receptor Information
>7r04 Chain A (length=2326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPVEWVQAVVSRFDEQLPIKTKVSTEHNKECLINISKYKFSLVISGLTTI
LKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKDTMRLDETMLVK
QLLPEICHFLHTCREGNQHAAELRNSASGVLFSLSCNNFNAVFSRISTRL
QELTVCSEDNVDVHDIELLQYINVDCAKLKRLLKETAFKFKALKKVAQLA
VINSLEKAFWNWVENYPDEFTKLYQIPQTDMAECAEKLFDLVDGFAESTK
RKAAVWPLQIILLILCPEIIQDISENNMNKKLFLDSLRKALAGHGGSRQL
TESAAIACVKLCKASTYINWEDNSVIFLLVQSMVVDLKNLLFNPSKPFSR
GSQPADVDLMIDCLVSCFRISPHNNQHFKICLAQNSPSTFHYVLVNSLHR
IITNSALDWWPKIDAVYCHSVELRNMFGETLHKAVQTRSYKYLLLSMVKL
IHADPKLLLCNPRKQGPETQGSTAELITGLVQLVPQSHMPEIAQEAMEAL
LVLHQLDSIDLWNPDAPVETFWEISSQMLFYICKKLTSHQMLSSTEILKW
LREILICRNKFLLKNKTPPICRQAQTKLEVALYMFLWNPDTEAVLVAMSC
FRHLCEEADIRCSVHNLLPNYNTFMEFASVSNMMSTGRAALQKRVMALLR
RIEHPTAGNTEAWEDTHAKWEQATKLILNDTDSLQEWINMTGFLCALGGV
CTPVSKFMDRLLSLMVCNHEKVGLQIRTNVKDLVGLELSPALYPMLFNKL
KNTISKFFDSQGQVLLTDTNTQFVEQTIAIMKNLLDNHTEGSSEHLGQAS
IETMMLNLVRYVRVLGNMVHAIQIKTKLCQLVEVMMARRDDLSFCQEMKF
RNKMVEYLTDWVMVKCLTRDLDQASMEAVVSLLAGLPLQPEEGDGVELME
AKSQLFLKYFTLFMNLLNDCSEMSRRLASLRHCTVLAMSNLLNANVDSGL
MHSIGLGYHKDLQTRATFMEVLTKILQQGTEFDTLAETVLADRFERLVEL
VTMMGDQGELPIAMALANVVPCSQWDELARVLVTLFDSRHLLYQLLWNMF
SKEVELADSMQTLFRGNSLASKIMTFCFKVYGATYLQKLLDPLLRIVITS
SDWQHVSFEVDPTRLEPSESLEENQRNLLQMTEKFFHAIISSSSEFPPQL
RSVCHCLYQVVSQRFPQNSIGAVGSAMFLRFINPAIVSPYEAGILDKKPP
PRIERGLKLMSKILQSIANHVLFTKEEHMRPFNDFVKSNFDAARRFFLDI
ASDLSFISDGNVLALHRLLWNNQEKIGQYLSSRRPFDKMATLLAYLGPPE
HKPVADTHWSSLNLTSSKFEEFMTRHQVHEKEEFKALKTLSIFYQAGTSK
AGNPIFYYVARRFKTGQINGDLLIYHVLLTLKPYYAKPYEIVVDLTHTGP
SNRFKTDFLSKWFVVFPGFAYDNVSAVYIYNCNSWVREYTKYHERLLTGL
KGSKRLVFIDCPGKLAEHIEHEQQKLPAATLALEEDLKVFHNALKLAHKD
TKVSIKVGSTAVQVTSAERTKVLGQSVFLNDIYYASEIEEICLVDENQFT
LTIANQGTPLTFMHQECEAIVQSIIHIRTRWELSQPDSIPQHTKIRPKDV
PGTLLNIALLNLGSSDPSLRSAAYNLLCALTCTFNLKIEGQLLETSGLCI
PANNTLFIVSISKTLAANEPHLTLEFLEECISGFSKSSIELKHLCLEYMT
PWLSNLVRFCKHNDDAKRQRVTAILDKLITMTINEKQMYPSIQAKIWGSL
GQITDLLDVVLDSFIKTSATGGLGSIKAEVMADTAVALASGNVKLVSSKV
IGRMCKIIDKTCLSPTPTLEQHLMWDDIAILARYMLMLSFNNSLDVAAHL
PYLFHVVTFLVATGPLSLRASTHGLVINIIHSLCTCSQLHFSEETKQVLR
LSLTEFSLPKFYLLFGISKVKSAAVIAFRSSYERETFALTSLETVTEALL
EIMEACMRDIPTCKWLDQWTELAQRFAFQYNPSLQPRALVVFGCISKRVS
HGQIKQIIRILSKALESCLKGPDTYNSQVLIEATVIALTKLQPLLNKDSP
LHKALFWVAVAVLQLDEVNLYSAGTALLEQNLHTLDSLRIFNDKSPEEVF
MAIRNPLEWHCKQMDHFVGLNFNSNFNFALVGHLLKGYRHPSPAIVARTV
RILHTLLTLVNKHRNCDKFEVNTQSVAYLAALLTVLLDEEVLTDPKIQAL
LLTVLATLVKYTTDEFDQRILYEYLAEASVVFPKVFPVVHNLLDSKINTL
LSLCQDPNLLNPIHGIVQSVVYHEESPPQYQTSYLQSFGFNGLWRFAGPF
SKQTQIPDYAELIVKFLDALIDTYLP
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(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)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain7r04 Chain A Residue 2901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure 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]
PDB7r04 Structural basis of activation of the tumor suppressor protein neurofibromin.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		R1207 Y1524 W1538 S1539 F1551
Binding residue
(residue number reindexed from 1)		R996 Y1295 W1309 S1310 F1322
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0008289 lipid binding
GO:0008429 phosphatidylethanolamine binding
GO:0031210 phosphatidylcholine binding
Biological Process
GO:0000165 MAPK cascade
GO:0001525 angiogenesis
GO:0001649 osteoblast differentiation
GO:0001656 metanephros development
GO:0001666 response to hypoxia
GO:0001889 liver development
GO:0001935 endothelial cell proliferation
GO:0001937 negative regulation of endothelial cell proliferation
GO:0001938 positive regulation of endothelial cell proliferation
GO:0001952 regulation of cell-matrix adhesion
GO:0001953 negative regulation of cell-matrix adhesion
GO:0002686 negative regulation of leukocyte migration
GO:0006469 negative regulation of protein kinase activity
GO:0006606 protein import into nucleus
GO:0006915 apoptotic process
GO:0007154 cell communication
GO:0007265 Ras protein signal transduction
GO:0007269 neurotransmitter secretion
GO:0007405 neuroblast proliferation
GO:0007406 negative regulation of neuroblast proliferation
GO:0007420 brain development
GO:0007422 peripheral nervous system development
GO:0007507 heart development
GO:0007519 skeletal muscle tissue development
GO:0008283 cell population proliferation
GO:0008285 negative regulation of cell population proliferation
GO:0008542 visual learning
GO:0008625 extrinsic apoptotic signaling pathway via death domain receptors
GO:0010468 regulation of gene expression
GO:0010626 negative regulation of Schwann cell proliferation
GO:0014009 glial cell proliferation
GO:0014010 Schwann cell proliferation
GO:0014044 Schwann cell development
GO:0016477 cell migration
GO:0016525 negative regulation of angiogenesis
GO:0016601 Rac protein signal transduction
GO:0021510 spinal cord development
GO:0021764 amygdala development
GO:0021897 forebrain astrocyte development
GO:0021915 neural tube development
GO:0021987 cerebral cortex development
GO:0022011 myelination in peripheral nervous system
GO:0030036 actin cytoskeleton organization
GO:0030198 extracellular matrix organization
GO:0030199 collagen fibril organization
GO:0030316 osteoclast differentiation
GO:0030325 adrenal gland development
GO:0030336 negative regulation of cell migration
GO:0032228 regulation of synaptic transmission, GABAergic
GO:0033024 mast cell apoptotic process
GO:0033027 positive regulation of mast cell apoptotic process
GO:0033028 myeloid cell apoptotic process
GO:0033034 positive regulation of myeloid cell apoptotic process
GO:0034605 cellular response to heat
GO:0035021 negative regulation of Rac protein signal transduction
GO:0036135 Schwann cell migration
GO:0042060 wound healing
GO:0042127 regulation of cell population proliferation
GO:0042308 negative regulation of protein import into nucleus
GO:0043065 positive regulation of apoptotic process
GO:0043087 regulation of GTPase activity
GO:0043407 negative regulation of MAP kinase activity
GO:0043408 regulation of MAPK cascade
GO:0043409 negative regulation of MAPK cascade
GO:0043473 pigmentation
GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0043525 positive regulation of neuron apoptotic process
GO:0043535 regulation of blood vessel endothelial cell migration
GO:0043547 positive regulation of GTPase activity
GO:0045124 regulation of bone resorption
GO:0045671 negative regulation of osteoclast differentiation
GO:0045685 regulation of glial cell differentiation
GO:0045762 positive regulation of adenylate cyclase activity
GO:0045765 regulation of angiogenesis
GO:0046580 negative regulation of Ras protein signal transduction
GO:0046929 negative regulation of neurotransmitter secretion
GO:0048144 fibroblast proliferation
GO:0048147 negative regulation of fibroblast proliferation
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0048485 sympathetic nervous system development
GO:0048593 camera-type eye morphogenesis
GO:0048708 astrocyte differentiation
GO:0048709 oligodendrocyte differentiation
GO:0048712 negative regulation of astrocyte differentiation
GO:0048715 negative regulation of oligodendrocyte differentiation
GO:0048745 smooth muscle tissue development
GO:0048820 hair follicle maturation
GO:0048844 artery morphogenesis
GO:0048853 forebrain morphogenesis
GO:0050890 cognition
GO:0051402 neuron apoptotic process
GO:0060253 negative regulation of glial cell proliferation
GO:0060291 long-term synaptic potentiation
GO:0061534 gamma-aminobutyric acid secretion, neurotransmission
GO:0061535 glutamate secretion, neurotransmission
GO:0070372 regulation of ERK1 and ERK2 cascade
GO:0070662 mast cell proliferation
GO:0070667 negative regulation of mast cell proliferation
GO:0071887 leukocyte apoptotic process
GO:0072089 stem cell proliferation
GO:0097192 extrinsic apoptotic signaling pathway in absence of ligand
GO:0097529 myeloid leukocyte migration
GO:0098597 observational learning
GO:0099175 regulation of postsynapse organization
GO:1900148 negative regulation of Schwann cell migration
GO:1900271 regulation of long-term synaptic potentiation
GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation
GO:1904738 vascular associated smooth muscle cell migration
GO:1904753 negative regulation of vascular associated smooth muscle cell migration
GO:1990874 vascular associated smooth muscle cell proliferation
GO:2000108 positive regulation of leukocyte apoptotic process
GO:2000647 negative regulation of stem cell proliferation
GO:2001241 positive regulation of extrinsic apoptotic signaling pathway in absence of ligand
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0098793 presynapse
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7r04, PDBe:7r04, PDBj:7r04
PDBsum7r04
PubMed35353986
UniProtP21359|NF1_HUMAN Neurofibromin (Gene Name=NF1)

[Back to BioLiP]