Target Binding Site Detail
Target General Information | Top | ||||
---|---|---|---|---|---|
Target ID | T85309 | Target Info | |||
Target Name | Cystathionine beta-synthase (CBS) | ||||
Synonyms | Serine sulfhydrase; Beta-thionase | ||||
Target Type | Clinical trial Target | ||||
Gene Name | CBS | ||||
Biochemical Class | Alpha-carbonic anhydrase | ||||
UniProt ID |
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: 4L3V Crystal structure of delta516-525 human cystathionine beta-synthase | ||||||
Method | X-ray diffraction | Resolution | 3.63 Å | Mutation | No | [1] |
PDB Sequence |
PLWIRPDAPS
50 RCTWQLGRPA60 SESPHHHTAP70 AKSPKILPDI80 LKKIGDTPMV90 RINKIGKKFG 100 LKCELLAKCE110 FFNAGGSVKD120 RISLRMIEDA130 ERDGTLKPGD140 TIIEPTSGNT 150 GIGLALAAAV160 RGYRCIIVMP170 EKMSSEKVDV180 LRALGAEIVR190 TPTNARFDSP 200 ESHVGVAWRL210 KNEIPNSHIL220 DQYRNASNPL230 AHYDTTADEI240 LQQCDGKLDM 250 LVASVGTGGT260 ITGIARKLKE270 KCPGCRIIGV280 DPEGSILAEP290 EELNQTEQTT 300 YEVEGIGYDF310 IPTVLDRTVV320 DKWFKSNDEE330 AFTFARMLIA340 QEGLLCGGSA 350 GSTVAVAVKA360 AQELQEGQRC370 VVILPDSVRN380 YMTKFLSDRW390 MLQKGFLKEE 400 DLTEKKPWWW410 HLRVQELGLS420 APLTVLPTIT430 CGHTIEILRE440 KGFDQAPVVD 450 EAGVILGMVT460 LGNMLSSLLA470 GKVQPSDQVG480 KVIYKQFKQI490 RLTDTLGRLS 500 HILEMDHFAL510 VVHERQMVFG532 VVTAIDLLNF542 VAAQERDQ
|
|||||
|
VAL118
4.554
LYS119
1.356
SER147
4.576
ASN149
2.531
ASN228
4.970
HIS232
4.473
SER254
3.558
VAL255
3.592
GLY256
2.611
THR257
2.593
GLY258
3.215
|
|||||
PDB ID: 4L0D Crystal structure of delta516-525 human cystathionine beta-synthase containing C-terminal 6xHis-tag | ||||||
Method | X-ray diffraction | Resolution | 2.97 Å | Mutation | Yes | [1] |
PDB Sequence |
PLWIRPDAPS
50 RCTWQLGRPA60 SESPHHHTAP70 AKSPKILPDI80 LKKIGDTPMV90 RINKIGKKFG 100 LKCELLAKCE110 FFNAGGSVKD120 RISLRMIEDA130 ERDGTLKPGD140 TIIEPTSGNT 150 GIGLALAAAV160 RGYRCIIVMP170 EKMSSEKVDV180 LRALGAEIVR190 TPTNARFDSP 200 ESHVGVAWRL210 KNEIPNSHIL220 DQYRNASNPL230 AHYDTTADEI240 LQQCDGKLDM 250 LVASVGTGGT260 ITGIARKLKE270 KCPGCRIIGV280 DPEGSILAEP290 EELNQTEQTT 300 YEVEGIGYDF310 IPTVLDRTVV320 DKWFKSNDEE330 AFTFARMLIA340 QEGLLCGGSA 350 GSTVAVAVKA360 AQELQEGQRC370 VVILPDSVRN380 YMTKFLSDRW390 MLQKGFLKEE 400 DTEKKPWWWH411 LRVQELGLSA421 PLTVLPTITC431 GHTIEILREK441 GFDQAPVVDE 451 AGVILGMVTL461 GNMLSSLLAG471 KVQPSDQVGK481 VIYKQFKQIR491 LTDTLGRLSH 501 ILEMDHFALV511 VHEQMVFGVV534 TAIDLLNFVA544 AQERDQ
|
|||||
|
VAL118
4.476
LYS119
1.401
SER147
4.819
ASN149
2.682
ASN228
4.879
HIS232
4.499
SER254
3.649
VAL255
3.258
GLY256
2.838
THR257
2.469
GLY258
3.136
|
|||||
PDB ID: 4PCU Crystal structure of delta516-525 E201S human cystathionine beta-synthase with AdoMet | ||||||
Method | X-ray diffraction | Resolution | 3.58 Å | Mutation | Yes | [2] |
PDB Sequence |
WIRPDAPSRC
52 TWQLGRPASE62 SPHHHTAPAK72 SPKILPDILK82 KIGDTPMVRI92 NKIGKKFGLK 102 CELLAKCEFF112 NAGGSVKDRI122 SLRMIEDAER132 DGTLKPGDTI142 IEPTSGNTGI 152 GLALAAAVRG162 YRCIIVMPEK172 MSSEKVDVLR182 ALGAEIVRTP192 ARFDSPSSHV 204 GVAWRLKNEI214 PNSHILDQYR224 NASNPLAHYD234 TTADEILQQC244 DGKLDMLVAS 254 VGTGGTITGI264 ARKLKEKCPG274 CRIIGVDPEG284 SILAEPEELN294 QTEQTTYEVE 304 GIGYDFIPTV314 LDRTVVDKWF324 KSNDEEAFTF334 ARMLIAQEGL344 LCGGSAGSTV 354 AVAVKAAQEL364 QEGQRCVVIL374 PDSVRNYMTK384 FLSDRWMLQK394 GFLKEEDLKK 406 PWWWHLRVQE416 LGLSAPLTVL426 PTITCGHTIE436 ILREKGFDQA446 PVVDEAGVIL 456 GMVTLGNMLS466 SLLAGKVQPS476 DQVGKVIYKQ486 FKQIRLTDTL496 GRLSHILEMD 506 HFALVVHEQM529 VFGVVTAIDL539 LNFVAA
|
|||||
|
VAL118
4.640
LYS119
1.564
ASN149
3.100
ASN228
4.321
HIS232
4.422
SER254
3.464
VAL255
4.201
GLY256
3.199
THR257
2.594
GLY258
3.113
|
|||||
PDB ID: 4L27 Crystal structure of delta1-39 and delta516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6xHis tag | ||||||
Method | X-ray diffraction | Resolution | 3.39 Å | Mutation | Yes | [1] |
PDB Sequence |
LWIRPDAPSR
51 CTWQLGRPAS61 ESPHHHTAPA71 KSPKILPDIL81 KKIGDTPMVR91 INKIGKKFGL 101 KCELLAKCEF111 FNAGGSVKDR121 ISLRMIEDAE131 RDGTLKPGDT141 IIEPTSGNTG 151 IGLALAAAVR161 GYRCIIVMPE171 KMSSEKVDVL181 RALGAEIVRT191 PTNARFDSPE 201 SHVGVAWRLK211 NEIPNSHILD221 QYRNASNPLA231 HYDTTADEIL241 QQCDGKLDML 251 VASVGTGGTI261 TGIARKLKEK271 CPGCRIIGVD281 PEGSILAEPE291 ELNQTEQTTY 301 EVEGIGYDFI311 PTVLDRTVVD321 KWFKSNDEEA331 FTFARMLIAQ341 EGLLCGGSAG 351 STVAVAVKAA361 QELQEGQRCV371 VILPDSVRNY381 MTKFLSDRWM391 LQKGFLKEED 401 EKKPWWWHLR413 VQELGLSAPL423 TVLPTITCGH433 TIEILREKGF443 NQAPVVDEGV 454 ILGMVTLGNM464 LSSLLAGKVQ474 PSDQVGKVIY484 KQFKQIRLTD494 TLGRLSHILE 504 MDHFALVVHE514 MVFGVVTAID538 LLNFVAAQER548
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .B:118 or .B:119 or .B:147 or .B:149 or .B:228 or .B:232 or .B:254 or .B:255 or .B:256 or .B:257 or .B:258 or .B:259 or .B:260 or .B:261 or .B:304 or .B:305 or .B:306 or .B:349 or .B:375 or .B:376 or .B:381; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL118
4.519
LYS119
1.266
SER147
3.632
ASN149
2.599
ASN228
4.829
HIS232
4.498
SER254
3.763
VAL255
3.479
GLY256
2.657
THR257
2.760
GLY258
3.270
|
|||||
PDB ID: 4L28 Crystal structure of delta516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6xHis tag | ||||||
Method | X-ray diffraction | Resolution | 2.63 Å | Mutation | Yes | [1] |
PDB Sequence |
LWIRPDAPSR
51 CTWQLGRPAS61 ESPHHHTAPA71 KSPKILPDIL81 KKIGDTPMVR91 INKIGKKFGL 101 KCELLAKCEF111 FNAGGSVKDR121 ISLRMIEDAE131 RDGTLKPGDT141 IIEPTSGNTG 151 IGLALAAAVR161 GYRCIIVMPE171 KMSSEKVDVL181 RALGAEIVRT191 PTNARFDSPE 201 SHVGVAWRLK211 NEIPNSHILD221 QYRNASNPLA231 HYDTTADEIL241 QQCDGKLDML 251 VASVGTGGTI261 TGIARKLKEK271 CPGCRIIGVD281 PEGSILAEPE291 ELNQTEQTTY 301 EVEGIGYDFI311 PTVLDRTVVD321 KWFKSNDEEA331 FTFARMLIAQ341 EGLLCGGSAG 351 STVAVAVKAA361 QELQEGQRCV371 VILPDSVRNY381 MTKFLSDRWM391 LQKGFLKEED 401 TEKKPWWWHL412 RVQELGLSAP422 LTVLPTITCG432 HTIEILREKG442 FNQAPVVDEA 452 GVILGMVTLG462 NMLSSLLAGK472 VQPSDQVGKV482 IYKQFKQIRL492 TDTLGRLSHI 502 LEMDHFALVV512 HEQMVFGVVT535 AIDLLNFVAA545 QER
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:149 or .A:232 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:304 or .A:305 or .A:306 or .A:349 or .A:375 or .A:376 or .A:381; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
PDB ID: 4COO Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution | ||||||
Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [3] |
PDB Sequence |
WIRPDAPSRC
52 TWQLGRPASE62 SPHHHTAPAK72 SPKILPDILK82 KIGDTPMVRI92 NKIGKKFGLK 102 CELLAKCEFF112 NAGGSVKDRI122 SLRMIEDAER132 DGTLKPGDTI142 IEPTSGNTGI 152 GLALAAAVRG162 YRCIIVMPEK172 MSSEKVDVLR182 ALGAEIVRTP192 TNARFDSPES 202 HVGVAWRLKN212 EIPNSHILDQ222 YRNASNPLAH232 YDTTADEILQ242 QCDGKLDMLV 252 ASVGTGGTIT262 GIARKLKEKC272 PGCRIIGVDP282 EGSILAEPEE292 LNQTEQTTYE 302 VEGIGYDFIP312 TVLDRTVVDK322 WFKSNDEEAF332 TFARMLIAQE342 GLLCGGSAGS 352 TVAVAVKAAQ362 ELQEGQRCVV372 ILPDSVRNYM382 TKFLSDRWML392 QKGFLKEEDL 402 TEKKPWWWHL412 RVQELGLSAP422 LTVLPTITCG432 HTIEILREKG442 FDQAPVVDEA 452 GVILGMVTLG462 NMLSSLLAGK472 VQPSDQVGKV482 IYKQFKQIRL492 TDTLGRLSHI 502 LEMDHFALVV512 HEQMVFGVVT535 AIDLLNFVAA545 QER
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:147 or .A:149 or .A:228 or .A:232 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:304 or .A:305 or .A:306 or .A:349 or .A:375 or .A:376 or .A:381; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL118
4.629
LYS119
1.631
SER147
4.724
ASN149
2.893
ASN228
4.686
HIS232
4.328
SER254
3.567
VAL255
3.696
GLY256
2.872
THR257
2.701
GLY258
2.865
|
|||||
PDB ID: 7QGT Crystal structure of human cystathionine beta-synthase (delta516-525) in complex with AOAA. | ||||||
Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [4] |
PDB Sequence |
PLWIRPDAPS
50 RCTWQLGRPA60 SESPHHHTAP70 AKSPKILPDI80 LKKIGDTPMV90 RINKIGKKFG 100 LKCELLAKCE110 FFNAGGSVKD120 RISLRMIEDA130 ERDGTLKPGD140 TIIEPTSGNT 150 GIGLALAAAV160 RGYRCIIVMP170 EKMSSEKVDV180 LRALGAEIVR190 TPTNARFDSP 200 ESHVGVAWRL210 KNEIPNSHIL220 DQYRNASNPL230 AHYDTTADEI240 LQQCDGKLDM 250 LVASVGTGGT260 ITGIARKLKE270 KCPGCRIIGV280 DPEGSILAEP290 EELNQTEQTT 300 YEVEGIGYDF310 IPTVLDRTVV320 DKWFKSNDEE330 AFTFARMLIA340 QEGLLCGGSA 350 GSTVAVAVKA360 AQELQEGQRC370 VVILPDSVRN380 YMTKFLSDRW390 MLQKGFLKEE 400 DLTEKKPWWW410 HLRVQELGLS420 APLTVLPTIT430 CGHTIEILRE440 KGFDQAPVVD 450 EAGVILGMVT460 LGNMLSSLLA470 GKVQPSDQVG480 KVIYKQFKQI490 RLTDTLGRLS 500 HILEMDHFAL510 VVHEQQRQMV520 FGVVTAIDLL530 NFVAAQERDQ540 |
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:147 or .A:149 or .A:228 or .A:232 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:304 or .A:305 or .A:306 or .A:349 or .A:375 or .A:376 or .A:381; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL118
4.941
LYS119
1.474
SER147
3.949
ASN149
3.097
ASN228
4.542
HIS232
4.269
SER254
3.699
VAL255
3.888
GLY256
3.054
THR257
2.788
GLY258
2.933
|
|||||
PDB ID: 1JBQ STRUCTURE OF HUMAN CYSTATHIONINE BETA-SYNTHASE: A UNIQUE PYRIDOXAL 5'-PHOSPHATE DEPENDENT HEMEPROTEIN | ||||||
Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [5] |
PDB Sequence |
WIRPDAPSRC
52 TWQLGRPASE62 SPHHHTAPAK72 SPKILPDILK82 KIGDTPMVRI92 NKIGKKFGLK 102 CELLAKCEFF112 NAGGSVKDRI122 SLRMIEDAER132 DGTLKPGDTI142 IEPTSGNTGI 152 GLALAAAVRG162 YRCIIVMPEK172 MSSEKVDVLR182 ALGAEIVRTP192 TESHVGVAWR 209 LKNEIPNSHI219 LDQYRNASNP229 LAHYDTTADE239 ILQQCDGKLD249 MLVASVGTGG 259 TITGIARKLK269 EKCPGCRIIG279 VDPEGSILAE289 PEELNQTEQT299 TYEVEGIGYD 309 FIPTVLDRTV319 VDKWFKSNDE329 EAFTFARMLI339 AQEGLLCGGS349 AGSTVAVAVK 359 AAQELQEGQR369 CVVILPDSVR379 NYMTKFLSDR389 WMLQKGFL
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:149 or .A:228 or .A:232 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:304 or .A:305 or .A:306 or .A:349 or .A:375 or .A:376 or .A:381; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL118
4.522
LYS119
1.269
ASN149
2.738
ASN228
4.843
HIS232
4.508
SER254
3.545
VAL255
3.481
GLY256
2.849
THR257
2.612
GLY258
3.260
|
|||||
PDB ID: 5MMS Human cystathionine beta-synthase (CBS) p.P49L delta409-551 variant | ||||||
Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | Yes | [6] |
PDB Sequence |
IRPDALSRCT
53 WQLGRPASES63 PHHHTAPAKS73 PKILPDILKK83 IGDTPMVRIN93 KIGKKFGLKC 103 ELLAKCEFFN113 AGGSVKDRIS123 LRMIEDAERD133 GTLKPGDTII143 EPTSGNTGIG 153 LALAAAVRGY163 RCIIVMPEKM173 SSEKVDVLRA183 LGAEIVRTPP200 ESHVGVAWRL 210 KNEIPNSHIL220 DQYRNASNPL230 AHYDTTADEI240 LQQCDGKLDM250 LVASVGTGGT 260 ITGIARKLKE270 KCPGCRIIGV280 DPEGSILAEP290 EELNYEVEGI306 GYDFIPTVLD 316 RTVVDKWFKS326 NDEEAFTFAR336 MLIAQEGLLC346 GGSAGSTVAV356 AVKAAQELQE 366 GQRCVVILPD376 SVRNYMTKFL386 SDRWMLQKGF396
|
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:149 or .A:228 or .A:232 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:304 or .A:305 or .A:306 or .A:349 or .A:375 or .A:376 or .A:381; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL118
4.409
LYS119
1.479
ASN149
2.917
ASN228
4.486
HIS232
4.250
SER254
3.672
VAL255
3.689
GLY256
2.991
THR257
2.677
GLY258
3.198
|
|||||
PDB ID: 1M54 CYSTATHIONINE-BETA SYNTHASE: REDUCED VICINAL THIOLS | ||||||
Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | Yes | [7] |
PDB Sequence |
DAPSRCTWQL
56 GRPASESPHH66 HTAPAKSPKI76 LPDILKKIGD86 TPMVRINKIG96 KKFGLKCELL 106 AKCEFFNAGG116 SVKDRISLRM126 IEDAERDGTL136 KPGDTIIEPT146 SGNTGIGLAL 156 AAAVRGYRCI166 IVMPEKMSSE176 KVDVLRALGA186 EIVRTPTNPE201 SHVGVAWRLK 211 NEIPNSHILD221 QYRNASNPLA231 HYDTTADEIL241 QQCDGKLDML251 VASVGTGGTI 261 TGIARKLKEK271 CPGCRIIGVD281 PEGSILAEPE291 ELNQTEQTTY301 EVEGIGYDFI 311 PTVLDRTVVD321 KWFKSNDEEA331 FTFARMLIAQ341 EGLLCGGSAG351 STVAVAVKAA 361 QELQEGQRCV371 VILPDSVRNY381 MTKFLSDRWM391 LQKGFLKEED401 LT |
|||||
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLP or .PLP2 or .PLP3 or :3PLP;style chemicals stick;color identity;select .A:118 or .A:119 or .A:149 or .A:228 or .A:232 or .A:254 or .A:255 or .A:256 or .A:257 or .A:258 or .A:259 or .A:260 or .A:261 or .A:304 or .A:305 or .A:306 or .A:349 or .A:375 or .A:376 or .A:381; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
VAL118
4.150
LYS119
1.456
ASN149
2.646
ASN228
4.488
HIS232
4.358
SER254
3.966
VAL255
3.628
GLY256
2.639
THR257
2.769
GLY258
3.143
|
References | Top | ||||
---|---|---|---|---|---|
REF 1 | Structural basis of regulation and oligomerization of human cystathionine beta-synthase, the central enzyme of transsulfuration. Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3790-9. | ||||
REF 2 | Structural insight into the molecular mechanism of allosteric activation of human cystathionine beta-synthase by S-adenosylmethionine. Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):E3845-52. | ||||
REF 3 | Inter-domain communication of human cystathionine beta-synthase: structural basis of S-adenosyl-L-methionine activation. J Biol Chem. 2014 Dec 26;289(52):36018-30. | ||||
REF 4 | H(2)S biogenesis by cystathionine beta-synthase: mechanism of inhibition by aminooxyacetic acid and unexpected role of serine. Cell Mol Life Sci. 2022 Jul 21;79(8):438. | ||||
REF 5 | Structure of human cystathionine beta-synthase: a unique pyridoxal 5'-phosphate-dependent heme protein. EMBO J. 2001 Aug 1;20(15):3910-6. | ||||
REF 6 | A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine beta-Synthase: Increased CO Reactivity as a Novel Molecular Mechanism of Pathogenicity?. Oxid Med Cell Longev. 2017;2017:8940321. | ||||
REF 7 | Human cystathionine beta-synthase is a heme sensor protein. Evidence that the redox sensor is heme and not the vicinal cysteines in the CXXC motif seen in the crystal structure of the truncated enzyme. Biochemistry. 2002 Aug 20;41(33):10454-61. |
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.