Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T78198 | Target Info | |||
| Target Name | Purine nucleoside phosphorylase (PNP) | ||||
| Synonyms | PNP; Inosine phosphorylase | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | PNP | ||||
| Biochemical Class | Pentosyltransferase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | DADMe-ImmG | Ligand Info | |||
| Canonical SMILES | C1C(C(CN1CC2=CNC3=C2N=C(NC3=O)N)O)CO | ||||
| InChI | 1S/C12H17N5O3/c13-12-15-9-6(1-14-10(9)11(20)16-12)2-17-3-7(5-18)8(19)4-17/h1,7-8,14,18-19H,2-5H2,(H3,13,15,16,20)/t7-,8+/m1/s1 | ||||
| InChIKey | GSPTUGDLYPMLCQ-SFYZADRCSA-N | ||||
| PubChem Compound ID | 135415984 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5UGF Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
MENGYTYEDY
10 KNTAEWLLSH20 TKHRPQVAII30 CGSGLGGLTD40 KLTQAQIFDY50 SEIPNFPRST 60 VPGHAGRLVF70 GFLNGRACVM80 MQGRFHMYEG90 YPLWKVTFPV100 RVFHLLGVDT 110 LVVTNAAGGL120 NPKFEVGDIM130 LIRDHINLPG140 FSGQNPLRGP150 NDERFGDRYP 160 AMSDAYDRTM170 RQRALSTWKQ180 MGEQRELQEG190 TYVMVAGPSF200 ETVAECRVLQ 210 KLGADAVGMS220 TVPEVIVARH230 CGLRVFGFSL240 ITNKVIMDYE250 SLEKANHEEV 260 LAAGKQAAQK270 LEQFVSILMA280 SIPLPD
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| PDB ID: 4EAR Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| PDB Sequence |
GYTYEDYKNT
13 AEYLLSHTKH23 RPQVAIICGS33 GLGGLTDKLT43 QAQIFDYSEI53 PNFPRSTVPG 63 HAGRLVFGFL73 NGRACVMMQG83 RFHMYEGYPL93 YKVTFPVRVF103 HLLGVDTLVV 113 TNAAGGLNPK123 FEVGDIMLIR133 DHINLPGFSG143 QNPLRGPNDE153 RFGDRFPAMS 163 DAYDRTMRQR173 ALSTYKQMGE183 QRELQEGTYV193 MVAGPSFETV203 AECRVLQKLG 213 ADAVGMSTVP223 EVIVARHCGL233 RVFGFSLITN243 KVIMDYESLE253 KANEEVLAAG 264 KQAAQKLEQF274 VSILMASIPL284 PD
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| PDB ID: 3PHB Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
PTLMENGYTY
7 EDYKNTAEWL17 LSHTKHRPQV27 AIICGSGLGG37 LTDKLTQAQI47 FDYSEIPNFP 57 RSTVPGHAGR67 LVFGFLNGRA77 CVMMQGRFHM87 YEGYPLWKVT97 FPVRVFHLLG 107 VDTLVVTNAA117 GGLNPKFEVG127 DIMLIRDHIN137 LPGFSGQNPL147 RGPNDERFGD 157 RFPAMSDAYD167 RTMRQRALST177 WKQMGEQREL187 QEGTYVMVAG197 PSFETVAECR 207 VLQKLGADAV217 GMSTVPEVIV227 ARHCGLRVFG237 FSLITNKVIM247 DYESLEKANH 257 EEVLAAGKQA267 AQKLEQFVSI277 LMASIPLP
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| PDB ID: 4EB8 Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [2] |
| PDB Sequence |
TLMENGYTYE
8 DYKNTAEYLL18 SHTKHRPQVA28 IICGSGLGGL38 TDKLTQAQIF48 DYSEIPNFPR 58 STVPGHAGRL68 VFGFLNGRAC78 VMMQGRFHMY88 EGYPLYKVTF98 PVRVFHLLGV 108 DTLVVTNAAG118 GLNPKFEVGD128 IMLIRDHINL138 PGFSGQNPLR148 GPNDERFGDR 158 FPAMSDAYDR168 TMRQRALSTY178 KQMGEQRELQ188 EGTYVMVAGP198 SFETVAECRV 208 LQKLGADAVG218 MSTVPEVIVA228 RHCGLRVFGF238 SLITNKVIMD248 YESLEKANWE 258 EVLAAGKQAA268 QKLEQFVSIL278 MASIPLPD
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IM5 or .IM52 or .IM53 or :3IM5;style chemicals stick;color identity;select .A:33 or .A:86 or .A:88 or .A:116 or .A:117 or .A:118 or .A:195 or .A:200 or .A:201 or .A:217 or .A:218 or .A:219 or .A:242 or .A:243 or .A:245 or .A:255 or .A:257 or .A:260; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5ETJ Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human complexed with DADMe-ImmG and phosphate | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [4] |
| PDB Sequence |
TLMENGYTYE
8 DYKNTAEWLL18 SHTKHRPQVA28 IICGSGLGGL38 TDKLTQAQIF48 DYSEIPNFPR 58 STVPGHAGRL68 VFGFLNGRAC78 VMMQGRFHMY88 EGYPLWKVTF98 PVRVFHLLGV 108 DTLVVTNAAG118 GLNPKFEVGD128 IMLIRDHINL138 PGFSGQNPLR148 GPNDERFGDR 158 FPAMSDAYDR168 TMRQRALSTW178 KQMGEQRELQ188 EGTYVMVAGP198 SFETVAECRV 208 LQKLGADAVG218 MSTVPEVIVA228 RHCGLRVFGF238 SLITNKVIMD248 YESLEKANHD 258 EVAAAGKQAA268 QKLEQFVSIL278 MASIPLPD
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IM5 or .IM52 or .IM53 or :3IM5;style chemicals stick;color identity;select .A:33 or .A:86 or .A:88 or .A:116 or .A:117 or .A:118 or .A:195 or .A:200 or .A:201 or .A:217 or .A:218 or .A:219 or .A:242 or .A:243 or .A:245 or .A:255 or .A:256 or .A:257 or .A:260; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase. Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6456-6461. | ||||
| REF 2 | Catalytic site conformations in human PNP by 19F-NMR and crystallography. Chem Biol. 2013 Feb 21;20(2):212-22. | ||||
| REF 3 | Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG | ||||
| REF 4 | Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics. J Am Chem Soc. 2016 Mar 16;138(10):3403-9. | ||||
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