Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T00477 Target Info
Target Name Serine Racemase (SRR)
Synonyms L-serine dehydratase; L-serine ammonia-lyase; D-serine dehydratase; D-serine ammonia-lyase
Target Type Literature-reported Target
Gene Name SRR
Biochemical Class Racemases and epimerase
UniProt ID
SRR_HUMAN
Ligand General Information  Top
Ligand Name Pyridoxal phosphate Ligand Info
Canonical SMILES CC1=NC=C(C(=C1O)C=O)COP(=O)(O)O
InChI 1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKey NGVDGCNFYWLIFO-UHFFFAOYSA-N
PubChem Compound ID 1051
Drug Binding Sites of Target  Top
PDB ID: 3L6B      X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor
Method X-ray diffraction Resolution 1.50 Å Mutation Yes [1]
PDB Sequence
AQYDISFADV
12
EKAHINIRDS
22
IHLTPVLTSS
32
ILNQLTGRNL
42
FFKCELFQKT
52

GSFKIRGALN
62
AVRSLVRKPK
77
AVVTHSSGNH
87
GQALTYAAKL
97
EGIPAYIVVP
107

QTAPDCKKLA
117
IQAYGASIVY
127
CEPSDESREN
137
VAKRVTEETE
147
GIMVHPNQEP
157

AVIAGQGTIA
167
LEVLNQVPLV
177
DALVVPVGGG
187
GMLAGIAITV
197
KALKPSVKVY
207

AAEPSNADDC
217
YQSKLKGKLM
227
PNLYPPETIA
237
DGVKSSIGLN
247
TWPIIRDLVD
257

DIFTVTEDEI
267
KCATQLVWER
277
MKLLIEPTAG
287
VGVAAVLSQH
297
FQTVSPEVKN
307

ICIVLSGGNV
317
DLTSSITWVK
327
QA
Residue
Distance (Å)
SER54
4.248
PHE55
3.415
LYS56
1.539
ASN86
2.913
PRO153
4.843
ASN154
4.046
PRO183
3.857
VAL184
3.783
GLY185
2.802
GLY186
3.013
GLY187
2.780
Residue
Distance (Å)
GLY188
2.836
MET189
2.886
LEU190
4.876
GLY239
4.039
VAL240
3.642
GLU283
3.692
THR285
3.234
ALA286
4.918
SER313
2.744
GLY314
3.629
PDB ID: 5X2L      Crystal Structure of Human Serine Racemase
Method X-ray diffraction Resolution 1.81 Å Mutation No [2]
PDB Sequence
AQYCISFADV
12
EKAHINIRDS
22
IHLTPVLTSS
32
ILNQLTGRNL
42
FFKCELFQKT
52

GSFKIRGALN
62
AVRSKAVVTH
82
SSGNHGQALT
92
YAAKLEGIPA
102
YIVVPQTAPD
112

CKKLAIQAYG
122
ASIVYCEPSD
132
ESRENVAKRV
142
TEETEGIMVH
152
PNQEPAVIAG
162

QGTIALEVLN
172
QVPLVDALVV
182
PVGGGGMLAG
192
IAITVKALKP
202
SVKVYAAEPS
212

NADDCYQSKL
222
KGKLMPNLYP
232
PETIADGVKS
242
SIGLNTWPII
252
RDLVDDIFTV
262

TEDEIKCATQ
272
LVWERMKLLI
282
EPTAGVGVAA
292
VLSQHFQTVS
302
PEVKNICIVL
312

SGGNV
Residue
Distance (Å)
SER54
4.525
PHE55
3.287
LYS56
1.467
ASN86
2.829
PRO153
4.776
ASN154
3.945
PRO183
4.122
VAL184
3.798
GLY185
2.770
GLY186
2.819
GLY187
2.736
Residue
Distance (Å)
GLY188
2.827
MET189
2.835
LEU190
4.891
GLY239
3.652
VAL240
3.760
GLU283
3.682
THR285
3.279
ALA286
4.930
SER313
2.652
GLY314
3.734
References  Top
REF 1 The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding. J Biol Chem. 2010 Apr 23;285(17):12873-81.
REF 2 Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase. Bioorg Med Chem Lett. 2018 Feb 1;28(3):441-445.

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