Structure of PDB 4b56 Chain A Binding Site BS03

Receptor Information
>4b56 Chain A (length=816) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KSCKGRCFERTFSNCRCDAACVSLGNCCLDFQETCVEPTHIWTCNKFRCG
EKRLSRFVCSCADDCKTHNDCCINYSSVCQDKKSWVEETCESIDTPECPA
EFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTK
TFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQP
IWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLE
WLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMD
GLKDLGLDKCLNLILISDHGMEQGSCKKYVYLNKYLGDVNNVKVVYGPAA
RLRPTDVPETYYSFNYEALAKNLSCREPNQHFRPYLKPFLPKRLHFAKSD
RIEPLTFYLDPQWQLALNPSERKYCGSGFHGSDNLFSNMQALFIGYGPAF
KHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPIYNPSHP
KEEGFLSQCPIKSTSNDLGCTCDPWIVPIKDFEKQLNLTTEDVDDIYHMT
VPYGRPRILLKQHHVCLLQQQQFLTGYSLDLLMPLWASYTFLRNDQFSRD
DFSNCLYQDLRIPLSPVHKCSYYKSNSKLSYGFLTPPRLNRVSNHIYSEA
LLTSNIVPMYQSFQVIWHYLHDTLLQRYAHERNGINVVSGPVFDFDYDGR
YDSLEILKQNSRVIRSQEILIPTHFFIVLTSCKQLSETPLECSALESSAY
ILPHRPDNIESCTHGKRESSWVEELLTLHRARVTDVELITGLSFYQDRQE
SVSELLRLKTHLPIFS
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain4b56 Chain A Residue 1003 [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]
PDB4b56 Structure of Npp1, an Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D781 D783 D785 R787 D789
Binding residue
(residue number reindexed from 1)		D694 D696 D698 R700 D702
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.1: phosphodiesterase I.
3.6.1.9: nucleotide diphosphatase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity
GO:0004528 phosphodiesterase I activity
GO:0004551 dinucleotide phosphatase activity
GO:0005509 calcium ion binding
GO:0008081 phosphoric diester hydrolase activity
GO:0008270 zinc ion binding
GO:0010945 coenzyme A diphosphatase activity
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0016791 phosphatase activity
GO:0036219 GTP diphosphatase activity
GO:0036221 UTP diphosphatase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0047429 nucleoside triphosphate diphosphatase activity
GO:0047693 ATP diphosphatase activity
GO:0106177 cyclic-GMP-AMP hydrolase activity
Biological Process
GO:0000902 cell morphogenesis
GO:0001503 ossification
GO:0001570 vasculogenesis
GO:0001649 osteoblast differentiation
GO:0001822 kidney development
GO:0001922 B-1 B cell homeostasis
GO:0001958 endochondral ossification
GO:0002009 morphogenesis of an epithelium
GO:0002021 response to dietary excess
GO:0002269 leukocyte activation involved in inflammatory response
GO:0002317 plasma cell differentiation
GO:0002437 inflammatory response to antigenic stimulus
GO:0006096 glycolytic process
GO:0006631 fatty acid metabolic process
GO:0007005 mitochondrion organization
GO:0007224 smoothened signaling pathway
GO:0007507 heart development
GO:0007605 sensory perception of sound
GO:0007628 adult walking behavior
GO:0008283 cell population proliferation
GO:0008340 determination of adult lifespan
GO:0008344 adult locomotory behavior
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0009611 response to wounding
GO:0010467 gene expression
GO:0010960 magnesium ion homeostasis
GO:0014004 microglia differentiation
GO:0015938 coenzyme A catabolic process
GO:0016055 Wnt signaling pathway
GO:0016192 vesicle-mediated transport
GO:0019634 organic phosphonate metabolic process
GO:0019725 cellular homeostasis
GO:0021510 spinal cord development
GO:0022010 central nervous system myelination
GO:0030217 T cell differentiation
GO:0030225 macrophage differentiation
GO:0030279 negative regulation of ossification
GO:0030282 bone mineralization
GO:0030316 osteoclast differentiation
GO:0030502 negative regulation of bone mineralization
GO:0030505 inorganic diphosphate transport
GO:0031103 axon regeneration
GO:0031214 biomineral tissue development
GO:0032026 response to magnesium ion
GO:0032868 response to insulin
GO:0034505 tooth mineralization
GO:0034516 response to vitamin B6
GO:0035128 post-embryonic forelimb morphogenesis
GO:0035264 multicellular organism growth
GO:0035630 bone mineralization involved in bone maturation
GO:0035904 aorta development
GO:0036076 ligamentous ossification
GO:0036119 response to platelet-derived growth factor
GO:0038065 collagen-activated signaling pathway
GO:0042445 hormone metabolic process
GO:0042474 middle ear morphogenesis
GO:0042476 odontogenesis
GO:0042593 glucose homeostasis
GO:0042789 mRNA transcription by RNA polymerase II
GO:0042832 defense response to protozoan
GO:0043588 skin development
GO:0045444 fat cell differentiation
GO:0045453 bone resorption
GO:0045599 negative regulation of fat cell differentiation
GO:0046034 ATP metabolic process
GO:0046323 D-glucose import
GO:0046716 muscle cell cellular homeostasis
GO:0046849 bone remodeling
GO:0050951 sensory perception of temperature stimulus
GO:0050954 sensory perception of mechanical stimulus
GO:0051216 cartilage development
GO:0051402 neuron apoptotic process
GO:0051649 establishment of localization in cell
GO:0055062 phosphate ion homeostasis
GO:0055074 calcium ion homeostasis
GO:0060291 long-term synaptic potentiation
GO:0060346 bone trabecula formation
GO:0060348 bone development
GO:0060350 endochondral bone morphogenesis
GO:0060612 adipose tissue development
GO:0060613 fat pad development
GO:0060840 artery development
GO:0061975 articular cartilage development
GO:0070212 protein poly-ADP-ribosylation
GO:0070254 mucus secretion
GO:0070640 vitamin D3 metabolic process
GO:0071344 diphosphate metabolic process
GO:0071529 cementum mineralization
GO:0097241 hematopoietic stem cell migration to bone marrow
GO:0097252 oligodendrocyte apoptotic process
GO:0098868 bone growth
GO:0140459 response to Gram-positive bacterium
GO:0140928 inhibition of non-skeletal tissue mineralization
GO:1902742 apoptotic process involved in development
GO:1904124 microglial cell migration
GO:1904383 response to sodium phosphate
GO:1904384 cellular response to sodium phosphate
GO:1904738 vascular associated smooth muscle cell migration
GO:1990787 negative regulation of hh target transcription factor activity
GO:1990874 vascular associated smooth muscle cell proliferation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016323 basolateral plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4b56, PDBe:4b56, PDBj:4b56
PDBsum4b56
PubMed23041369
UniProtP06802|ENPP1_MOUSE Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (Gene Name=Enpp1)

[Back to BioLiP]