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Receptor
PDB id Resolution Class Description Source Keywords
5IFK 1.97 Å EC: 2.4.2.1 PURINE NUCLEOSIDE PHOSPHORYLASE KLUYVEROMYCES LACTIS (STRAIN ATCC 85852359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) PURINE NUCLEOSIDE PHOSPHORYLASE HYPOXANTHINE NP-I FAMILY KLUYVEROMYCES LACTIS TRANSFERASE
Ref.: FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF PURIN NUCLEOSIDE PHOSPHORYLASE FROM KLUYVEROMYCES LACTIS POTENTIAL APPLICATIONS IN REDUCING PURINE CONTENT I PLOS ONE V. 11 64279 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HPA C:401;
B:401;
A:401;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
136.111 C5 H4 N4 O c1[nH...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IFK 1.97 Å EC: 2.4.2.1 PURINE NUCLEOSIDE PHOSPHORYLASE KLUYVEROMYCES LACTIS (STRAIN ATCC 85852359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) PURINE NUCLEOSIDE PHOSPHORYLASE HYPOXANTHINE NP-I FAMILY KLUYVEROMYCES LACTIS TRANSFERASE
Ref.: FUNCTIONAL AND STRUCTURAL CHARACTERIZATION OF PURIN NUCLEOSIDE PHOSPHORYLASE FROM KLUYVEROMYCES LACTIS POTENTIAL APPLICATIONS IN REDUCING PURINE CONTENT I PLOS ONE V. 11 64279 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5IFK - HPA C5 H4 N4 O c1[nH]c2c(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5IFK - HPA C5 H4 N4 O c1[nH]c2c(....
50% Homology Family (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ON6 Ki = 172 nM IMH C11 H14 N4 O4 c1c(c2c([n....
2 2A0Y Ki = 900 pM DIH C12 H17 N4 O3 c1c(c2c([n....
3 1RR6 - IMH C11 H14 N4 O4 c1c(c2c([n....
4 2A0X Ki = 950 pM DIH C12 H17 N4 O3 c1c(c2c([n....
5 3GB9 - A2F C5 H4 F N5 c1[nH]c2c(....
6 1RT9 - IMH C11 H14 N4 O4 c1c(c2c([n....
7 5UGF - IM5 C12 H17 N5 O3 c1c(c2c([n....
8 3BGS Ki = 380 pM DIH C12 H17 N4 O3 c1c(c2c([n....
9 1RSZ - DIH C12 H17 N4 O3 c1c(c2c([n....
10 2A0W Ki = 270 pM DIH C12 H17 N4 O3 c1c(c2c([n....
11 1B8O Ki = 23 pM IMH C11 H14 N4 O4 c1c(c2c([n....
12 1A9T - R1P C5 H11 O8 P C([C@@H]1[....
13 1VFN Ki = 2.5 uM HPA C5 H4 N4 O c1[nH]c2c(....
14 2QPL ic50 = 18.9 uM BTY C6 H7 N5 O Cc1cc2n(n1....
15 2AI1 ic50 = 300 nM P1G C12 H16 N5 O8 P c1nc2c(n1[....
16 1B8N Ki = 30 pM IMG C11 H15 N5 O4 c1c(c2c([n....
17 1A9S - NOS C10 H12 N4 O5 c1nc2c(n1[....
18 2AI3 ic50 = 5000 nM P2G C11 H14 N5 O8 P c1nc2c(n1[....
19 1LVU Kd = 4.8 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
20 1A9P - 9DI C11 H13 N3 O5 c1c(c2c([n....
21 2AI2 ic50 = 30 nM P1D C13 H16 N3 O8 P c1c(c2c([n....
22 1V48 Ki = 16 nM HA1 C10 H14 F2 N5 O4 P c1nc2c(n1C....
23 1A9Q - HPA C5 H4 N4 O c1[nH]c2c(....
24 3FUC Kd = 190 pM 9D9 9DG n/a n/a
25 1A9R - HPA C5 H4 N4 O c1[nH]c2c(....
26 1LV8 Kd = 3.5 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
27 1FXU - GU7 C10 H16 N6 O3 c1nc2c(n1C....
28 5IFK - HPA C5 H4 N4 O c1[nH]c2c(....
29 5TBT - CTN C9 H13 N3 O5 C1=CN(C(=O....
30 5TBU - HPA C5 H4 N4 O c1[nH]c2c(....
31 5TBS - ADE C5 H5 N5 c1[nH]c2c(....
32 4EAR - IM5 C12 H17 N5 O3 c1c(c2c([n....
33 5ETJ Kd = 66 pM IM5 C12 H17 N5 O3 c1c(c2c([n....
34 4EB8 - IM5 C12 H17 N5 O3 c1c(c2c([n....
35 2P4S Kd = 0.42 nM DIH C12 H17 N4 O3 c1c(c2c([n....
36 3FB1 - R1P C5 H11 O8 P C([C@@H]1[....
37 3E9R - ADE C5 H5 N5 c1[nH]c2c(....
38 3E0Q - JFD C4 H4 Br N3 O2 C1(=C(NC(=....
39 3FNQ - HPA C5 H4 N4 O c1[nH]c2c(....
40 3FAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
41 3IEX - GMP C10 H13 N5 O5 c1nc2c(n1[....
42 3DJF ic50 = 0.8 uM BC3 C12 H11 N5 O c1cc(cnc1)....
43 3F8W - ADN C10 H13 N5 O4 c1nc(c2c(n....
44 1VMK - GUN C5 H5 N5 O c1[nH]c2c(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HPA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 HPA 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IFK; Ligand: HPA; Similar sites found with APoc: 268
This union binding pocket(no: 1) in the query (biounit: 5ifk.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2PTM CMP None
2 1Q7B NAP None
3 2X06 NAD 0.961538
4 2APC UDM 1.28205
5 3C3N FMN 1.28205
6 6B2M COA 1.3986
7 6CI9 NAP 1.5444
8 3OIX FMN 1.60256
9 3SHR CMP 1.67224
10 6C5F 7L9 1.7094
11 2C78 PUL 1.92308
12 3VZ3 NAP 1.92308
13 4ZVV NAD 1.92308
14 4ZVV GN0 1.92308
15 3VZ3 SSN 1.92308
16 3ETG GLU 1.92308
17 3ETG NDP 1.92308
18 1TDF FAD 1.92308
19 3MJY FMN 1.92308
20 3MJY IJZ 1.92308
21 3IWK NAD 1.92308
22 3LXK MI1 1.92308
23 5X1M DHB 1.92308
24 5X1M THG 1.92308
25 5BV6 35G 1.97368
26 5JJU AMP 2.24359
27 3EFV NAD 2.24359
28 5U3F 7TS 2.24359
29 5L13 6ZE 2.24359
30 2IV2 2MD 2.24359
31 5DNC ASN 2.24359
32 1K97 ASP 2.24359
33 1K97 CIR 2.24359
34 1QS8 IVA VAL VAL STA ALA STA 2.24359
35 1GQG DCD 2.24359
36 4R8L ASP 2.24359
37 5O7E 9NB 2.24359
38 3G6K POP 2.27273
39 3G6K FAD 2.27273
40 4L2I NAD 2.28137
41 4L2I FAD 2.28137
42 2WSI FAD 2.28758
43 4PFW MAN MAN BMA BMA BMA BMA 2.3766
44 4I8P NAD 2.5
45 1IA9 ANP 2.5
46 5IUW IAC 2.5641
47 5IUW NAD 2.5641
48 4CE5 PDG 2.5641
49 5X5U NAD 2.5641
50 1E5Q SHR 2.5641
51 1DL5 SAH 2.5641
52 1DJN FMN 2.5641
53 4B0T ADP 2.5641
54 3HQP OXL 2.5641
55 1LLU NAD 2.5641
56 4IDT T28 2.5641
57 4PJT 2YQ 2.5641
58 1Q19 APC 2.88462
59 3HLF SIM 2.88462
60 2RCU BUJ 2.88462
61 5KF6 NAD 2.88462
62 2Y5D NAP 2.88462
63 1EFY BZC 2.88462
64 1PHP ADP 2.88462
65 4FER CE6 2.88462
66 1Q8A HCS 2.88462
67 1IYE PGU 2.91262
68 3EUF BAU 3.04878
69 1EFV AMP 3.13725
70 1EFV FAD 3.13725
71 6H21 UD1 3.18841
72 4UUG PXG 3.20513
73 3VGL ANP 3.20513
74 4I3V NAD 3.20513
75 4B2Z P5S 3.20513
76 3UDZ ADP 3.20513
77 2GMH FAD 3.20513
78 2IHK CSF 3.20513
79 2IV3 UDP 3.20513
80 2GMH UQ5 3.20513
81 4YRY FAD 3.26087
82 4GJ3 0XP 3.31126
83 2J9D AMP 3.36134
84 2C5S AMP 3.38983
85 2II3 CAO 3.43511
86 2YNE YNE 3.52564
87 2YNE NHW 3.52564
88 3JZ4 NAP 3.52564
89 5ECP MET 3.52564
90 5ECP JAA 3.52564
91 5ECP ATP 3.52564
92 1K3T BRZ 3.52564
93 3MKH FAD 3.52564
94 4BR5 ANP 3.52564
95 1VPE ANP 3.52564
96 4YJK URA 3.57143
97 1ZUI SKM 3.57143
98 5J6D 6H5 3.58306
99 5JAX 6J7 3.7037
100 4TXJ THM 3.71622
101 1XK9 P34 3.72093
102 5W5R PYR 3.82775
103 1T90 NAD 3.84615
104 1O9J NAD 3.84615
105 2WOX NDP 3.84615
106 1YP4 ADP 3.84615
107 3JDW ORN 3.84615
108 1YFS ALA 3.84615
109 3ZNN 4WL 3.84615
110 3ZNN FAD 3.84615
111 4LH0 GLV 3.84615
112 3HBF MYC 3.84615
113 3HBF UDP 3.84615
114 4GYW UDP 3.84615
115 5BNW 12V 3.84615
116 3B82 NAD 3.86473
117 1B1C FMN 3.8674
118 5NII FAD 3.8835
119 5D2H AKG 3.88693
120 3VYW SAM 3.8961
121 1S4M LUM 4.09556
122 6B5G NAD 4.16667
123 4ZUL UN1 4.16667
124 6B5G CQY 4.16667
125 1QF5 RPL 4.16667
126 1QF5 GDP 4.16667
127 1YNH SUO 4.16667
128 1G51 AMO 4.16667
129 5F7N NAG GAL FUC FUC A2G 4.16667
130 5JXZ ISC 4.16667
131 5EOU ATP 4.16667
132 1GPM AMP 4.16667
133 5F7Y GLC GAL NAG GAL FUC A2G 4.16667
134 3OH3 UAD 4.16667
135 2E0N SAH 4.2471
136 6AA8 NAD 4.30464
137 3EYA TDP 4.48718
138 2BO4 FLC 4.48718
139 3EYA FAD 4.48718
140 5B47 PYR 4.48718
141 5B47 TPP 4.48718
142 4M7V RAR 4.57143
143 5HXI 5HN 4.74934
144 5HXI FAD 4.74934
145 4R84 CSF 4.77137
146 2XIQ MLC 4.80769
147 2BJK NAD 4.80769
148 3UZO PLP 4.80769
149 5ERR ADP 4.80769
150 3UZO GLU 4.80769
151 1N07 ADP 4.90798
152 3ZF8 GDP 4.91803
153 5THY SAH 4.93827
154 5K9B FMN 5
155 3WIS FMN 5.02513
156 4NJS G08 5.05051
157 1SBZ FMN 5.07614
158 1JE1 GMP 5.08475
159 5KZD RCJ 5.11945
160 1KQF MGD 5.12821
161 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 5.12821
162 2YYJ FAD 5.12821
163 2YYJ 4HP 5.12821
164 4Z9D NAD 5.14286
165 3P0F BAU 5.38721
166 1EYQ NAR 5.40541
167 6BQC LOP 5.44872
168 1RJW ETF 5.44872
169 5XFV FMN 5.44872
170 5THZ SAH 5.44872
171 1J3I NDP 5.4878
172 1ODJ GMP 5.53191
173 6BHV DQV 5.53506
174 6F5Z SAH 5.62771
175 1ZOS MTM 5.65217
176 1JGT APC 5.76923
177 1JGT CMA 5.76923
178 5N5S NAP 5.76923
179 2XXP DSL 5.76923
180 1WDK NAD 5.76923
181 2E7Z MGD 5.76923
182 2WBP SIN 5.86592
183 2WBP ZZU 5.86592
184 4BMX ADE 5.9761
185 2RDE C2E 5.9761
186 4PZ2 NAD 6.08974
187 3D91 REM 6.08974
188 4QIJ 1HA 6.08974
189 5I60 67W 6.08974
190 3HAZ NAD 6.08974
191 3LF0 ATP 6.14035
192 5O0B 9FE 6.17284
193 4YC0 5OF 6.27615
194 1KOR ANP 6.41026
195 1KOR ARG 6.41026
196 1KOR SIN 6.41026
197 2R75 01G 6.41026
198 5X8G S0N 6.41026
199 5K3W PLP 6.41026
200 3KJD 78P 6.41026
201 3KYG 5GP 5GP 6.60793
202 3LZW FAD 6.73077
203 1XHC FAD 6.73077
204 5JFL NAD 6.73077
205 1UA4 GLC 6.73077
206 1UA4 BGC 6.73077
207 3BW2 FMN 6.77507
208 3BJE URA 7.05128
209 4D9M 0JO 7.05128
210 5W75 SUC 7.05128
211 4PAB THG 7.05128
212 1D4D FAD 7.37179
213 4MSG 2C6 7.37327
214 1RM6 PCD 7.45342
215 5L9O GOP 7.46269
216 5Y4R C2E 7.48299
217 5C8W PCG 7.69231
218 6AMI TRP 7.69231
219 3KVY URA 7.76699
220 6GAS FAD 8.01282
221 5WAN FMN 8.01282
222 3A16 PXO 8.01282
223 3BL6 FMC 8.26087
224 5HW4 SAM 8.46774
225 5ZJ5 NAI 8.64198
226 1CT9 AMP 8.65385
227 1CT9 GLN 8.65385
228 5C5H 4YB 8.65385
229 2A5F NAD 8.80829
230 1G63 FMN 8.83978
231 1U1F 183 8.97436
232 5YSI NCA 9.21053
233 5EYP GDP 9.61539
234 1HXD BTN 9.9359
235 3LGS SAH 10.1124
236 3LGS ADE 10.1124
237 3AB1 FAD 10.2564
238 4RR7 A3S 10.2941
239 4WKB TDI 10.5769
240 1EZ0 NAP 10.5769
241 5UCD NAP 10.8974
242 3RHJ NAP 11.2179
243 4FFS BIG 11.2971
244 4QAR ADE 11.4428
245 3G5K BB2 11.4754
246 2QV6 GTP 11.5672
247 5ITZ GTP 11.811
248 3NWQ 2NC 12.1212
249 4OFG PCG 12.5
250 2C6Q NDP 12.8205
251 2C6Q IMP 12.8205
252 5T2Z 017 13.1313
253 4WKC BIG 13.8776
254 6AYR BIG 14.2857
255 3DLG GWE 14.3182
256 1BVY FMN 16.7539
257 3RYC GTP 16.7832
258 5UKL SIX 17.7419
259 4R3U 3HC 19.6203
260 4R3U 3KK 19.6203
261 1H0H 2MD 20.1923
262 3QPB URA 21.9858
263 5F7J ADE 28.2051
264 5CLO NS8 30.5085
265 1K27 MTM 30.7421
266 4GLJ RHB 33.67
267 1C3X 8IG 37.9699
268 2A8Y MTA 41.1111
Pocket No.: 2; Query (leader) PDB : 5IFK; Ligand: HPA; Similar sites found with APoc: 74
This union binding pocket(no: 2) in the query (biounit: 5ifk.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1U1B PAX None
2 6BA2 7KM 1.69492
3 3O26 NDP 1.92926
4 4MUV PCG 2.11268
5 1OVD ORO 2.24359
6 1OVD FMN 2.24359
7 6MPT C30 2.44755
8 2V2V V12 2.58303
9 4N9I PCG 2.85714
10 4CQM NAP 2.86885
11 5MZI FAD 2.88462
12 5MZI FYK 2.88462
13 6BKA FMN 2.88462
14 6CC0 EWM 2.95359
15 2OQ2 A3P 3.06513
16 2YC5 6BC 3.07018
17 4JNA FAD 3.20513
18 1XJD STU 3.20513
19 4ZH7 FUC GAL NAG GAL FUC 3.20513
20 4M2K PLP 3.20513
21 4KU7 PCG 3.26797
22 4DXD 9PC 3.28283
23 2J9D ADP 3.36134
24 4XOQ F42 3.38164
25 1AKV FMN 3.40136
26 3ESS 18N 3.47826
27 5L2M 6ZY 3.52564
28 1NZY BCA 3.71747
29 2AQX ATP 3.80623
30 2WME NAP 3.84615
31 3QXV MTX 3.96825
32 1AG9 FMN 4
33 3T4L ZEA 4.07407
34 4IMG NGF 4.09556
35 3AXB FAD 4.16667
36 3AXB PRO 4.16667
37 1KYZ SAH 4.16667
38 1MJH ATP 4.32099
39 5GM1 SAH 4.3771
40 1L3I SAH 4.48718
41 2D0O ADP 4.80769
42 4H2D FMN 4.84848
43 5O4J SAH 5.10949
44 5O4J PJL 5.10949
45 6GNF ADP 5.12821
46 5B48 TDN 5.2459
47 6C74 PC 5.40541
48 2OYS FMN 5.78512
49 5FA6 FAD 6.08974
50 5FA6 FMN 6.08974
51 4HEQ FMN 6.16438
52 2QHV OC9 6.19048
53 3L9R L9R 6.36042
54 5O0J GLC 6.73077
55 2WC1 FMN 7.14286
56 1O94 AMP 7.37179
57 1O97 AMP 7.37179
58 1O97 FAD 7.37179
59 4C3Y FAD 7.69231
60 3GPO APR 7.7381
61 5XLY C2E 7.82918
62 6AM8 PLT 8.01282
63 2BNE U5P 8.71369
64 2BL9 NDP 8.82353
65 2BL9 CP6 8.82353
66 2ZMF CMP 9.52381
67 5HI5 63Q 9.84848
68 1JUV NDP 10.8808
69 4X3R 686 10.8974
70 1RLJ FMN 11.5108
71 1M3U KPL 14.1026
72 4NPT 017 14.1414
73 3CX5 SMA 15.1351
74 3CF6 SP1 25.1497
Pocket No.: 3; Query (leader) PDB : 5IFK; Ligand: HPA; Similar sites found with APoc: 21
This union binding pocket(no: 3) in the query (biounit: 5ifk.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3O9Z AKG 1.92308
2 1Q0S SAH 2.3166
3 2JAJ D20 2.42215
4 2D4V NAD 2.88462
5 2IVD ACJ 3.20513
6 4E3Q PMP 3.84615
7 3RS8 APR 4.48718
8 1Y8Q ATP 4.80769
9 5AYV KPL 4.85437
10 1X7D ORN 5.12821
11 6FKW PQQ 5.76923
12 1O68 KIV 5.81818
13 3QV1 NAD 6.09756
14 2Q7V FAD 6.41026
15 3LZW NAP 6.73077
16 1E3W NAD 7.27969
17 4UBT 3G6 7.37179
18 3NJ4 NAD 7.69231
19 3WOL VAL TYR 8.65385
20 2O4N TPV 14.1414
21 1EX7 5GP 15.0538
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