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 T10877 Target Info
Target Name Cyclic ADP-ribose hydrolase 1 (CD38)
Synonyms cADPr hydrolase 1; T10; Cyclic ADPribose hydrolase 1; ADPribosyl cyclase 1; ADPRC 1; ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1; ADP-ribosyl cyclase 1; 2'-phospho-cyclic-ADP-ribose transferase; 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase; 2'-phospho-ADP-ribosyl cyclase
Target Type Successful Target
Gene Name CD38
Biochemical Class Glycosylase
UniProt ID
CD38_HUMAN
Ligand General Information  Top
Ligand Name ara-2'F-ADPR Ligand Info
Canonical SMILES C1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=NC4=C(N=CN=C43)N)O)O)O)F
InChI 1S/C15H22FN5O12P2/c16-6-1-29-7(10(6)22)2-30-34(25,26)33-35(27,28)31-3-8-11(23)12(24)15(32-8)21-5-20-9-13(17)18-4-19-14(9)21/h4-8,10-12,15,22-24H,1-3H2,(H,25,26)(H,27,28)(H2,17,18,19)/t6-,7-,8-,10+,11-,12-,15-/m1/s1
InChIKey GOCJJDZHXMDJEZ-WFCIOUKESA-N
PubChem Compound ID 49866653
Drug Binding Sites of Target  Top
PDB ID: 3I9M      Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR
Method X-ray diffraction Resolution 1.75 Å Mutation Yes [1]
PDB Sequence
RWRQTWSGPG
54
TTKRFPETVL
64
ARCVKYTEIH
74
PEMRHVDCQS
84
VWDAFKGAFI
94

SKHPCDITEE
104
DYQPLMKLGT
114
QTVPCNKILL
124
WSRIKDLAHQ
134
FTQVQRDMFT
144

LEDTLLGYLA
154
DDLTWCGEFD
164
TSKINYQSCP
174
DWRKDCSNNP
184
VSVFWKTVSR
194

RFAEAACDVV
204
HVMLDGSRSK
214
IFDKDSTFGS
224
VEVHNLQPEK
234
VQTLEAWVIH
244

GGREDSRDLC
254
QDPTIKELES
264
IISKRNIQFS
274
CKNIYRPDKF
284
LQCVKNPEDS
294

SC
Residue
Distance (Å)
TRP125
3.277
SER126
2.657
ARG127
2.758
LYS129
3.509
LEU145
4.304
GLU146
3.002
ALA154
4.366
ASP155
2.805
ASP156
2.936
LEU157
4.559
Residue
Distance (Å)
VAL185
4.154
SER186
3.782
TRP189
3.334
SER193
2.670
ASP219
4.884
SER220
3.107
THR221
2.616
PHE222
3.347
GLU226
1.568
PDB ID: 3OFS      Dynamic conformations of the CD38-mediated NAD cyclization captured using multi-copy crystallography
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [2]
PDB Sequence
WRQTWSGPGT
55
TKRFPETVLA
65
RCVKYTEIHP
75
EMRHVDCQSV
85
WDAFKGAFIS
95

KHPCDITEED
105
YQPLMKLGTQ
115
TVPCNKILLW
125
SRIKDLAHQF
135
TQVQRDMFTL
145

ADTLLGYLAD
155
DLTWCGEFDT
165
SKINYQSCPD
175
WRKDCSNNPV
185
SVFWKTVSRR
195

FAEAACDVVH
205
VMLDGSRSKI
215
FDKDSTFGSV
225
EVHNLQPEKV
235
QTLEAWVIHG
245

EDSRDLCQDP
257
TIKELESIIS
267
KRNIQFSCKN
277
IYRP
Residue
Distance (Å)
LEU123
4.905
LEU124
3.652
TRP125
2.757
SER126
2.714
ARG127
2.366
LYS129
3.422
LEU145
3.270
ALA146
4.621
GLY151
4.905
ALA154
4.783
ASP155
2.917
Residue
Distance (Å)
ASP156
3.137
VAL185
3.940
SER186
3.938
TRP189
3.199
SER193
3.093
PHE196
3.898
SER220
3.136
THR221
2.865
PHE222
3.277
GLY223
4.935
GLU226
1.581
References  Top
REF 1 Structural basis for enzymatic evolution from a dedicated ADP-ribosyl cyclase to a multifunctional NAD hydrolase. J Biol Chem. 2009 Oct 2;284(40):27637-45.
REF 2 Dynamic conformations of the CD38-mediated NAD cyclization captured in a single crystal. J Mol Biol. 2011 Jan 28;405(4):1070-8.

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