Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T47466 Target Info
Target Name Porphobilinogen deaminase (HMBS)
Synonyms Preuroporphyrinogen synthase; PBGD; Hydroxymethylbilane synthase; HMBS
Target Type Clinical trial Target
Gene Name HMBS
Biochemical Class Alkyl aryl transferase
UniProt ID
HEM3_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: 3-[5-[[3-(2-carboxyethyl)-5-[[3-(2-carboxyethyl)-5-[[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid Ligand Info
Structure Description Human porphobilinogen deaminase R173W mutant crystallized in the ES2 intermediate state PDB:7AAK
Method X-ray diffraction Resolution 1.70 Å Mutation Yes [1]
PDB Sequence
KMRVIRVGTR
26
KSQLARIQTD
36
SVVATLKASY
46
PGLQFEIIAM
56
STTGDKILDT
66

ALSKIGEKSL
76
FTKELEHALE
86
KNEVDLVVHS
96
LKDLPTVLPP
106
GFTIGAICKR
116

ENPHDAVVFH
126
PKFVGKTLET
136
LPEKSVVGTS
146
SLRRAAQLQR
156
KFPHLEFRSI
166

RGNLNTWLRK
176
LDEQQEFSAI
186
ILATAGLQRM
196
GWHNRVGQIL
206
HPEECMYAVG
216

QGALGVEVRA
226
KDQDILDLVG
236
VLHDPETLLR
246
CIAERAFLRH
256
LEGGCSVPVA
266

VHTAMKDGQL
276
YLTGGVWSLD
286
GSDSIQETMQ
296
ATIHVPAQHE
306
DGPEDDPQLV
316

GITARNIPRG
326
PQLAAQNLGI
336
SLANLLLSKG
346
AKNILDVARQ
356
LNDAH
Residue
Distance (Å)
LEU30
4.547
GLN34
4.241
ILE71
3.762
LYS74
2.970
SER75
3.482
SER96
2.788
LEU97
4.480
LYS98
2.663
ASP99
2.858
LEU100
3.605
PRO101
3.665
THR102
2.746
VAL103
4.304
SER146
4.210
SER147
2.798
ARG149
2.820
ARG150
2.674
Residue
Distance (Å)
LEU188
3.600
ALA189
2.879
ALA191
4.456
GLY192
4.354
ARG195
2.952
ALA214
3.594
VAL215
2.719
GLY216
4.703
GLN217
3.500
GLY218
2.987
ALA219
4.949
ARG251
4.528
LEU254
3.645
GLY259
4.162
GLY260
4.320
CYS261
1.769
SER262
3.120
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: 3-[5-{[3-(2-Carboxyethyl)-4-(Carboxymethyl)-5-Methyl-1h-Pyrrol-2-Yl]methyl}-4-(Carboxymethyl)-1h-Pyrrol-3-Yl]propanoic Acid Ligand Info
Structure Description Human porphobilinogen deaminase in complex with cofactor PDB:7AAJ
Method X-ray diffraction Resolution 1.80 Å Mutation No [1]
PDB Sequence
KMRVIRVGTR
26
KSQLARIQTD
36
SVVATLKASY
46
PGLQFEIIAM
56
SSLFTKELEH
83

ALEKNEVDLV
93
VHSLKDLPTV
103
LPPGFTIGAI
113
CKRENPHDAV
123
VFHPKFVGKT
133

LETLPEKSVV
143
GTSSLRRAAQ
153
LQRKFPHLEF
163
RSIRGNLNTR
173
LRKLDEQQEF
183

SAIILATAGL
193
QRMGWHNRVG
203
QILHPEECMY
213
AVGQGALGVE
223
VRAKDQDILD
233

LVGVLHDPET
243
LLRCIAERAF
253
LRHLEGGCSV
263
PVAVHTAMKD
273
GQLYLTGGVW
283

SLDGSDSIQE
293
TMQATIHVPA
303
QHEDGPEDDP
313
QLVGITARNI
323
PRGPQLAAQN
333

LGISLANLLL
343
SKGAKNILDV
353
ARQL
Residue
Distance (Å)
LEU30
4.138
GLN34
3.698
SER96
2.747
LYS98
2.665
ASP99
2.999
THR145
3.516
SER146
3.266
SER147
2.821
ARG149
2.666
ARG150
3.057
ILE166
4.221
LEU170
4.240
Residue
Distance (Å)
ARG173
2.463
LEU188
3.539
ALA189
2.623
ALA191
4.780
GLY192
4.437
ARG195
3.502
ALA214
3.809
GLY216
4.830
GLN217
3.700
GLY218
3.055
LEU220
4.909
CYS261
1.766
Click to View More Binding Site Information of This Target and Ligand Pair
References  Top
REF 1 Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism. iScience. 2021 Feb 6;24(3):102152.

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