Structure of PDB 5dou Chain D Binding Site BS05

Receptor Information
>5dou Chain D (length=1430) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQTAHIVLEDGTKMKGYSFGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQ
ILTMANPIIGNGGAPDTTALDELGLSKYLESNGIKVSGLLVLDYSKDYNH
WLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTMLGKIEFEGQPVDF
VDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGAEV
HLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFG
ISTGNLITGLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALD
NTLPAGWKPLFVNVNDQTNEGIMHESKPFFAVQFHPEVTPGPIDTEYLFD
SFFSLIKKGKATTITSVLPKPALVASRVEVSKVLILGSGGLSIGQAGEFD
YSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQADTVYFLPITPQFV
TEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVESIM
ATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYAL
GGLGSGICPNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADD
NCVTVCNMENVDAMGVHTGDSVVVAPAQTLSNAEFQMLRRTSINVVRHLG
IVGECNIQFALHPTSMEYCIIEVNARLSRSSALASKATGYPLAFIAAKIA
LGIPLPEIKNVVSGKTSACFEPSLDYMVTKIPRWDLDRFHGTSSRIGSSM
KSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDLRKE
LSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLK
GLNSESMTEETLKRAKEIGFSDKQISKCLGLTEAQTRELRLKKNIHPWVK
QIDTLAAEYPSVTNYLYVTYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEF
DWCAVSSIRTLRQLGKKTVVVNCNPETVSTDFDECDKLYFEELSLERILD
IYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTSPLQIDRAEDRSIF
SAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRMNVVFSEDEMKKF
LEHPVVLTKFVEGAREVEMDAVGKDGRVISHAISEHVEDAGVHSGDATLM
LPTQTISQGAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLR
ASRSFPFVSKTLGVDFIDVATKVMIGENVDEKHLPTLDHPIIPADYVAIK
APMFSWPRLRDADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQ
KGILIGIQQSFRPRFLGVAEQLHNEGFKLFATEATSDWLNANNVPATPVA
WPSQEGQNPSLSSIRKLIRDGSIDLVINLPNNNTKFVHDNYVIRRTAVDS
GIPLLTNFQVTKLFAEAVQKDSKSLFHYRQ
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5dou Chain D Residue 2009 [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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PDB5dou Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		L1127 F1169 V1170 E1175 A1199 V1201 H1202 S1203 Q1243 L1245 I1254 E1255
Binding residue
(residue number reindexed from 1)		L1085 F1110 V1111 E1116 A1140 V1142 H1143 S1144 Q1184 L1186 I1195 E1196
Annotation score5
Enzymatic activity
Gene Ontology
Molecular Function
GO:0004087 carbamoyl-phosphate synthase (ammonia) activity
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
GO:0004175 endopeptidase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005543 phospholipid binding
GO:0016595 glutamate binding
GO:0016874 ligase activity
GO:0030955 potassium ion binding
GO:0036094 small molecule binding
GO:0044877 protein-containing complex binding
GO:0046872 metal ion binding
GO:0072341 modified amino acid binding
Biological Process
GO:0000050 urea cycle
GO:0001889 liver development
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006541 glutamine metabolic process
GO:0007494 midgut development
GO:0009410 response to xenobiotic stimulus
GO:0009636 response to toxic substance
GO:0010043 response to zinc ion
GO:0014075 response to amine
GO:0019240 citrulline biosynthetic process
GO:0019433 triglyceride catabolic process
GO:0019637 organophosphate metabolic process
GO:0032094 response to food
GO:0032496 response to lipopolysaccharide
GO:0033762 response to glucagon
GO:0034201 response to oleic acid
GO:0042311 vasodilation
GO:0042594 response to starvation
GO:0043200 response to amino acid
GO:0044344 cellular response to fibroblast growth factor stimulus
GO:0046209 nitric oxide metabolic process
GO:0048545 response to steroid hormone
GO:0050667 homocysteine metabolic process
GO:0051384 response to glucocorticoid
GO:0051591 response to cAMP
GO:0055081 monoatomic anion homeostasis
GO:0060416 response to growth hormone
GO:0070365 hepatocyte differentiation
GO:0070409 carbamoyl phosphate biosynthetic process
GO:0071242 cellular response to ammonium ion
GO:0071320 cellular response to cAMP
GO:0071377 cellular response to glucagon stimulus
GO:0071400 cellular response to oleic acid
GO:0071548 response to dexamethasone
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005886 plasma membrane
GO:0032991 protein-containing complex
GO:0042645 mitochondrial nucleoid

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dou, PDBe:5dou, PDBj:5dou
PDBsum5dou
PubMed26592762
UniProtP31327|CPSM_HUMAN Carbamoyl-phosphate synthase [ammonia], mitochondrial (Gene Name=CPS1)

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