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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SPHINGOSINE-1-PHOSPHATE LYASE IN COMPLEX WITH INHIBITOR 6-[(2R)-4-(4-BENZYL-7-CHLOROPHTHALAZIN-1-YL)-2-METHYLPIPERAZIN-1-YL]PYRIDINE-3-CARBONITRILE
 
Authors :  H. Srinivas
Date :  23 Apr 14  (Deposition) - 21 May 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plp, Pyridoxal 5-Phosphate-Dependent Enzymes, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Weiler, N. Braendlin, C. Beerli, C. Bergsdorf, A. Schubart, H. Srinivas, B. Oberhauser, A. Billich
Orally Active 7-Substituted (4-Benzylphthalazin-1-Yl)-2-Methylpiperazin-1- Yl]Nicotinonitriles As Active-Site Inhibitors Of Sphingosin 1-Phosphate Lyase For The Treatment Of Multiple Sclerosis.
J. Med. Chem. V. 57 5074 2014
PubMed-ID: 24809814  |  Reference-DOI: 10.1021/JM500338N

(-) Compounds

Molecule 1 - SPHINGOSINE-1-PHOSPHATE LYASE 1
    Chains: A, B
    EC Number: 4.1.2.27
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: KIAA1252, SGPL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: S1PL, SP-LYASE 1, SPL 1, HSPL, SPHINGOSINE-1-PHOSPHATE ALDOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
130J2Ligand/Ion6-[(2R)-4-(4-BENZYL-7-CHLOROPHTHALAZIN-1-YL)-2-METHYLPIPERAZIN-1-YL]PYRIDINE-3-CARBONITRILE
2GOL1Ligand/IonGLYCEROL
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4PO41Ligand/IonPHOSPHATE ION
5SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:148 , TYR A:150 , HIS A:242 , PHE A:290 , LLP A:353 , HOH A:1176 , HOH A:1177 , HIS B:174 , TYR B:387 , 30J B:602BINDING SITE FOR RESIDUE SIN A 901
2AC2SOFTWAREARG A:462 , ASN A:465 , LYS A:518 , THR A:519 , THR A:520BINDING SITE FOR RESIDUE GOL A 902
3AC3SOFTWARELEU A:173 , PRO A:175 , ILE A:386 , TYR A:387 , ALA A:388 , MET B:528 , VAL B:538 , LEU B:541 , SER B:542 , PHE B:545BINDING SITE FOR RESIDUE 30J A 903
4AC4SOFTWAREASN A:171 , HIS A:174 , THR B:148 , TYR B:150 , LLP B:353 , HOH B:854BINDING SITE FOR RESIDUE PO4 B 601
5AC5SOFTWAREILE A:525 , VAL A:538 , LEU A:541 , SER A:542 , PHE A:545 , SIN A:901 , LEU B:173 , ILE B:386 , TYR B:387 , ALA B:388BINDING SITE FOR RESIDUE 30J B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q6R)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:287 -Pro A:288
2Phe A:479 -Pro A:480
3Thr B:287 -Pro B:288
4Phe B:479 -Pro B:480

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q6R)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q6R)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeee........hhhhhhh.....eeeeeee..........hhhhhhhhhhhhh..eeeee..hhhhhh...................eeeeee............eeeee.hhhhhh...eee.......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.......eeeee.....hhhhhhhhhhh....eee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6r A 111 EYVKALPSQGLSSSAVLEKLKEYSSMDAFWQEGRASGTVYSGEEKLTELLVKAYGDFAWSNPLHPDIFPGLRKIEAEIVRIACSLFNGGPDSCGCVTSGGTESILMACKAYRDLAFEKGIKTPEIVAPQSAHAAFNKAASYFGMKIVRVPLTKMMEVDVRAMRRAISRNTAMLVCSTPQFPHGVIDPVPEVAKLAVKYKIPLHVDACLGGFLIVFMEKAGYPLEHPFDFRVKGVTSISADTHkYGYAPKGSSLVLYSDKKYRNYQFFVDTDWQGGIYASPTIAGSRPGGISAACWAALMHFGENGYVEATKQIIKTARFLKSELENIKGIFVFGNPQLSVIALGSRDFDIYRLSNLMTAKGWNLNQLQFPPSIHFCITLLHARKRVAIQFLKDIRESVTQIMKNPKAKTTGMGAIYGMAQTTVDRNMVAELSSVFLDSLYSTD 553
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  |    360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550   
                                                                                                                                                                                                                                                                            353-LLP                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh..eeeee..hhhhhh...................eeeeee............eeeee.hhhhhh...eee.......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.......eeeee.....hhhhhhhhhhh....eee....eeeee.hhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q6r B 110 KEYVKALPSQGLSSSAVLEKLKEYSSMDAFWQEGRASGTVYSGEEKLTELLVKAYGDFAWSNPLHPDIFPGLRKIEAEIVRIACSLFNGGPDSCGCVTSGGTESILMACKAYRDLAFEKGIKTPEIVAPQSAHAAFNKAASYFGMKIVRVPLTKMMEVDVRAMRRAISRNTAMLVCSTPQFPHGVIDPVPEVAKLAVKYKIPLHVDACLGGFLIVFMEKAGYPLEHPFDFRVKGVTSISADTHkYGYAPKGSSLVLYSDKKYRNYQFFVDTDWQGGIYASPTIAGSRPGGISAACWAALMHFGENGYVEATKQIIKTARFLKSELENIKGIFVFGNPQLSVIALGSRDFDIYRLSNLMTAKGWNLNQLQFPPSIHFCITLLHARKRVAIQFLKDIRESVTQIMKNPKAKTTGMGAIYGMAQTTVDRNMVAELSSVFLDSLYSTD 553
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   |   359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549    
                                                                                                                                                                                                                                                                             353-LLP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4Q6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q6R)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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1hbx 3mc6