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 T06958 Target Info
Target Name DNA polymerase beta (POLB)
Target Type Clinical trial Target
Gene Name POLB
UniProt ID
DPOLB_HUMAN
Ligand General Information  Top
Ligand Name [[(2r,5s)-5-(4-Azanyl-5-Fluoranyl-2-Oxidanylidene-Pyrimidin-1-Yl)-1,3-Oxathiolan-2-Yl]methoxy-Oxidanyl-Phosphoryl] Phosphono Hydrogen Phosphate Ligand Info
Canonical SMILES C1C(OC(S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
InChI 1S/C8H13FN3O12P3S/c9-4-1-12(8(13)11-7(4)10)5-3-28-6(22-5)2-21-26(17,18)24-27(19,20)23-25(14,15)16/h1,5-6H,2-3H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t5-,6+/m0/s1
InChIKey WIEOLFZNMKSGEX-NTSWFWBYSA-N
PubChem Compound ID 469172
Drug Binding Sites of Target  Top
PDB ID: 5U2T      Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+.
Method X-ray diffraction Resolution 1.79 Å Mutation No [1]
PDB Sequence
APQETLNGGI
15
TDMLTELANF
25
EKNVSQAIHK
35
YNAYRKAASV
45
IAKYPHKIKS
55

GAEAKKLPGV
65
GTKIAEKIDE
75
FLATGKLRKL
85
EKIRQDDTSS
95
SINFLTRVSG
105

IGPSAARKFV
115
DEGIKTLEDL
125
RKNEDKLNHH
135
QRIGLKYFGD
145
FEKRIPREEM
155

LQMQDIVLNE
165
VKKVDSEYIA
175
TVCGSFRRGA
185
ESSGDMDVLL
195
THPSFTSESP
208

KLLHQVVEQL
218
QKVHFITDTL
228
SKGETKFMGV
238
CQLPSKNDEK
248
EYPHRRIDIR
258

LIPKDQYYCG
268
VLYFTGSDIF
278
NKNMRAHAKG
290
FTINEYTIRP
300
LGVTGVAGEP
310

LPVDSEKDIF
320
DYIQWKYREP
330
KDRS
Residue
Distance (Å)
ARG149
3.015
GLY179
3.336
SER180
2.676
ARG183
2.873
SER187
4.734
SER188
3.618
GLY189
2.950
ASP190
3.277
Residue
Distance (Å)
ASP192
3.183
TYR271
3.260
PHE272
3.874
THR273
4.602
GLY274
4.067
SER275
4.256
ASP276
3.207
ASN279
3.710
PDB ID: 5TB9      Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)FTC-TP and Mn2+.
Method X-ray diffraction Resolution 2.49 Å Mutation No [2]
PDB Sequence
ETLNGGITDM
18
LTELANFEKN
28
VSQAIHKYNA
38
YRKAASVIAK
48
YPHKIKSGAE
58

AKKLPGVGTK
68
IAEKIDEFLA
78
TGKLRKLEKI
88
RQDDTSSSIN
98
FLTRVSGIGP
108

SAARKFVDEG
118
IKTLEDLRKN
128
EDKLNHHQRI
138
GLKYFGDFEK
148
RIPREEMLQM
158

QDIVLNEVKK
168
VDSEYIATVC
178
GSFRRGAESS
188
GDMDVLLTHP
198
SFTSESTKLL
211

HQVVEQLQKV
221
HFITDTLSKG
231
ETKFMGVCQL
241
PSKNEYPHRR
254
IDIRLIPKDQ
264

YYCGVLYFTG
274
SDIFNKNMRA
284
HALEKGFTIN
294
EYTIRPLGVT
304
GVAGEPLPVD
314

SEKDIFDYIQ
324
WKYREPKDRS
334
EHHHHHH
Residue
Distance (Å)
ARG149
4.188
GLY179
3.367
SER180
2.593
ARG183
2.995
SER187
4.965
SER188
3.548
GLY189
2.728
ASP190
2.484
ASP192
2.785
Residue
Distance (Å)
ASP256
3.817
TYR271
3.204
PHE272
3.382
THR273
4.530
GLY274
3.948
SER275
4.324
ASP276
3.317
ASN279
2.846
References  Top
REF 1 Structural basis for the D-stereoselectivity of human DNA polymerase beta. Nucleic Acids Res. 2017 Jun 2;45(10):6228-6237.
REF 2 Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J Am Chem Soc. 2017 Jan 11;139(1):465-471.

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