Receptor
PDB id Resolution Class Description Source Keywords
5MX4 2.31 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF H. PYLORI PURINE NUCLEOSIDE PHOSPHORYLA CLINICAL ISOLATE HPPNP-1 HELICOBACTER PYLORI R018C PURINE NUCLEOSIDE PHOSPHORYLASE CLINICAL ISOLATE HELICOBACPYLORI DEAD-END-COMPLEX TRANSFERASE
Ref.: STRUCTURAL CHARACTERIZATION OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM HUMAN PATHOGEN HELICOBACTER PYLO INT. J. BIOL. MACROMOL. V. 101 518 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 C:301;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
HPA C:300;
Valid;
none;
submit data
136.111 C5 H4 N4 O c1[nH...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5MX4 2.31 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF H. PYLORI PURINE NUCLEOSIDE PHOSPHORYLA CLINICAL ISOLATE HPPNP-1 HELICOBACTER PYLORI R018C PURINE NUCLEOSIDE PHOSPHORYLASE CLINICAL ISOLATE HELICOBACPYLORI DEAD-END-COMPLEX TRANSFERASE
Ref.: STRUCTURAL CHARACTERIZATION OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM HUMAN PATHOGEN HELICOBACTER PYLO INT. J. BIOL. MACROMOL. V. 101 518 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
2 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
3 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
70% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1Z35 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
2 1Z34 ic50 = 0.42 mM 2FD C10 H12 F N5 O3 c1nc2c(nc(....
3 1Z38 - NOS C10 H12 N4 O5 c1nc2c(n1[....
4 1PR1 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
5 1OUM - TAL C12 H16 N4 O4 Cc1c2c(ncn....
6 1PR2 - MDR C11 H14 N4 O3 Cc1c2c(ncn....
7 1PR5 Ki = 120 uM TBN C11 H14 N4 O4 c1cn(c2c1c....
8 1PKE - 2FD C10 H12 F N5 O3 c1nc2c(nc(....
9 1PR6 - XYA C10 H13 N5 O4 c1nc(c2c(n....
10 1PR0 - NOS C10 H12 N4 O5 c1nc2c(n1[....
11 1PK9 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
12 1OV6 - DBM C12 H16 N4 O4 Cc1c2c(ncn....
13 1PR4 - MTP C11 H14 N4 O4 S CSc1c2c(nc....
14 1PK7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
15 1OVG - MDR C11 H14 N4 O3 Cc1c2c(ncn....
16 1OU4 - 6MP C6 H6 N4 Cc1c2c(nc[....
17 1OTY - 6MP C6 H6 N4 Cc1c2c(nc[....
18 3UT6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
19 1PW7 - RAB C10 H13 N5 O4 c1nc(c2c(n....
20 1K9S - FM2 C11 H16 N5 O4 C[n+]1cnc2....
21 1A69 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
22 1VHW - ADN C10 H13 N5 O4 c1nc(c2c(n....
23 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
24 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
25 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
26 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
27 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
28 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
29 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
30 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
32 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
33 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
34 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
35 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
36 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
37 4DAB - 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 1Z35 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
2 1Z34 ic50 = 0.42 mM 2FD C10 H12 F N5 O3 c1nc2c(nc(....
3 1Z38 - NOS C10 H12 N4 O5 c1nc2c(n1[....
4 1PR1 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
5 1OUM - TAL C12 H16 N4 O4 Cc1c2c(ncn....
6 1PR2 - MDR C11 H14 N4 O3 Cc1c2c(ncn....
7 1PR5 Ki = 120 uM TBN C11 H14 N4 O4 c1cn(c2c1c....
8 1PKE - 2FD C10 H12 F N5 O3 c1nc2c(nc(....
9 1PR6 - XYA C10 H13 N5 O4 c1nc(c2c(n....
10 1PR0 - NOS C10 H12 N4 O5 c1nc2c(n1[....
11 1PK9 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
12 1OV6 - DBM C12 H16 N4 O4 Cc1c2c(ncn....
13 1PR4 - MTP C11 H14 N4 O4 S CSc1c2c(nc....
14 1PK7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
15 1OVG - MDR C11 H14 N4 O3 Cc1c2c(ncn....
16 1OU4 - 6MP C6 H6 N4 Cc1c2c(nc[....
17 1OTY - 6MP C6 H6 N4 Cc1c2c(nc[....
18 3UT6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
19 1PW7 - RAB C10 H13 N5 O4 c1nc(c2c(n....
20 1K9S - FM2 C11 H16 N5 O4 C[n+]1cnc2....
21 1A69 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
22 1VHW - ADN C10 H13 N5 O4 c1nc(c2c(n....
23 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
24 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
25 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
26 1JDV - ADN C10 H13 N5 O4 c1nc(c2c(n....
27 1JDT - MTA C11 H15 N5 O3 S CSC[C@@H]1....
28 1JE1 - GMP C10 H13 N5 O5 c1nc2c(n1[....
29 1JDZ - FMB C10 H12 N4 O5 C1=Nc2c(n[....
30 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
32 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
33 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
34 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
35 1ODI Kd = 62 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
36 1ODJ Kd = 80 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
37 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
38 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
39 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
40 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
41 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
43 4DAB - HPA C5 H4 N4 O c1[nH]c2c(....
44 3U40 - ADN C10 H13 N5 O4 c1nc(c2c(n....
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 : 5MX4; Ligand: HPA; Similar sites found: 214
This union binding pocket(no: 1) in the query (biounit: 5mx4.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QXV MTX 0.00885 0.42353 None
2 1U1B PAX 0.01777 0.42183 None
3 2ZIF SAM 0.01585 0.41359 None
4 4M7V RAR 0.04565 0.41088 None
5 1EQ2 NAP 0.03192 0.41034 None
6 5HWV MBN 0.007472 0.41034 None
7 1PNO NAP 0.0462 0.40174 1.66667
8 5LD5 NAD 0.01213 0.42607 1.71674
9 3A16 PXO 0.00109 0.411 1.71674
10 5XDT MB3 0.005644 0.45449 2.14592
11 2FK8 SAM 0.01784 0.41455 2.14592
12 4XTX 590 0.04373 0.40167 2.14592
13 2QRD ADP 0.01143 0.41919 2.18978
14 1KQP ADJ 0.04762 0.41248 2.21402
15 5IXG OTP 0.04205 0.41464 2.36686
16 3SUD SUE 0.04718 0.40455 2.46305
17 2C78 PUL 0.0006857 0.529 2.57511
18 1JV1 UD1 0.001118 0.49137 2.57511
19 5K3W PLP 0.002956 0.45083 2.57511
20 1CT9 AMP 0.002823 0.43865 2.57511
21 4YMH SAH 0.008969 0.43063 2.57511
22 4RKC PMP 0.007125 0.42484 2.57511
23 5C5H 4YB 0.01968 0.41986 2.57511
24 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.005745 0.41841 2.57511
25 3VC1 GST 0.04402 0.41272 2.57511
26 3VC1 SAH 0.04402 0.41272 2.57511
27 1KPG SAH 0.02583 0.40482 2.57511
28 1KPH SAH 0.0282 0.40477 2.57511
29 1OMO NAD 0.0333 0.40362 2.57511
30 2A9K NAD 0.01121 0.42667 2.69058
31 1OJZ NAD 0.008558 0.42811 2.83019
32 1GZF NAD 0.01617 0.41373 2.8436
33 1GZF NIR 0.008349 0.41232 2.8436
34 1GZF ADP 0.01564 0.41188 2.8436
35 1XNG ATP 0.003302 0.44703 3.00429
36 3DLG GWE 0.0188 0.44501 3.00429
37 5EWK P34 0.001833 0.4448 3.00429
38 4ITH RCM 0.007854 0.43435 3.00429
39 5KVA SAM 0.01003 0.42868 3.00429
40 3CMC NAD 0.04505 0.42833 3.00429
41 4R6W SAH 0.02117 0.42249 3.00429
42 4R6W PC 0.04281 0.42044 3.00429
43 2PZ8 APC 0.01291 0.41991 3.00429
44 2HNK SAH 0.01525 0.41654 3.00429
45 2RDE C2E 0.007761 0.414 3.00429
46 5LOG SAH 0.02061 0.40626 3.00429
47 1T90 NAD 0.03422 0.40569 3.00429
48 3X0D SAH 0.02511 0.40447 3.00429
49 2G30 ALA ALA PHE 0.001966 0.40001 3.00429
50 2BZG SAH 0.02335 0.40371 3.01724
51 3TAY MN0 0.01268 0.42036 3.06748
52 1HFS L04 0.01118 0.46458 3.125
53 2J9D AMP 0.001162 0.46947 3.36134
54 2J9D ADP 0.008209 0.42873 3.36134
55 2XIQ MLC 0.001173 0.48905 3.43348
56 4BKJ STI 0.02227 0.42219 3.43348
57 1OVD ORO 0.02635 0.41992 3.43348
58 1OVD FMN 0.02635 0.41992 3.43348
59 4PAB THG 0.01341 0.41362 3.43348
60 3VZ3 SSN 0.03165 0.41005 3.43348
61 1GQG DCD 0.01838 0.40892 3.43348
62 5TVA AMP 0.0113 0.40806 3.43348
63 3VZ3 NAP 0.02993 0.40687 3.43348
64 3VSE SAH 0.01563 0.40608 3.43348
65 2PA4 UPG 0.04612 0.40321 3.43348
66 5KJW 53C 0.01013 0.40108 3.43348
67 5M3E APR 0.006942 0.44619 3.63636
68 5U3F 7TS 0.001121 0.48033 3.86266
69 4B2Z P5S 0.004686 0.46033 3.86266
70 1Q19 APC 0.002694 0.45602 3.86266
71 4ZH7 FUC GAL NAG GAL FUC 0.00364 0.43576 3.86266
72 1I8T FAD 0.01505 0.43529 3.86266
73 5CCM 4ZX 0.0333 0.42141 3.86266
74 5CCM SAM 0.02815 0.42141 3.86266
75 3QV1 NAD 0.01667 0.42032 3.86266
76 4Q4K FMN 0.02839 0.40811 3.86266
77 4AUT FAD 0.04807 0.40769 3.86266
78 1WG8 SAM 0.03314 0.40109 3.86266
79 5N5D SAM 0.01107 0.4244 3.9823
80 1IIU RTL 0.0206 0.40719 4.02299
81 1L3I SAH 0.01928 0.41642 4.16667
82 1VKF CIT 0.005101 0.41689 4.25532
83 4R38 RBF 0.02741 0.4024 4.28571
84 3ILR SGN IXD 0.0227 0.43731 4.29185
85 3FIU AMP 0.003309 0.43598 4.29185
86 2YQS UD1 0.01013 0.4354 4.29185
87 1EFV FAD 0.0333 0.42975 4.29185
88 1EFV AMP 0.03355 0.42957 4.29185
89 1U2Z SAH 0.02714 0.40844 4.29185
90 2JAH NDP 0.02982 0.40762 4.29185
91 4N1T 2GD 0.01319 0.43361 4.40252
92 4RT1 C2E 0.009461 0.41744 4.46429
93 4QAR ADE 0.00000005588 0.69098 4.47761
94 1MDC PLM 0.01983 0.40836 4.54545
95 2XXP DSL 0.006332 0.47595 4.72103
96 2WN6 NDP 0.0132 0.41427 4.72103
97 5UAV NDP 0.04318 0.40947 4.72103
98 5UAV TFB 0.04318 0.40947 4.72103
99 3EFS BTN 0.02394 0.40182 4.72103
100 2ZMF CMP 0.001386 0.46862 4.7619
101 3HVJ 705 0.009263 0.44764 4.97738
102 4MSG 2C6 0.03161 0.41804 5.06912
103 3G6K POP 0.01561 0.42452 5.15021
104 3G6K FAD 0.01719 0.42452 5.15021
105 4ZUL UN1 0.04123 0.41167 5.15021
106 4CQM NAP 0.03684 0.40607 5.15021
107 3ESS 18N 0.004968 0.41982 5.21739
108 1OG1 TAD 0.02021 0.41233 5.30973
109 1REQ DCA 0.003481 0.47484 5.5794
110 4UUG PXG 0.002025 0.47106 5.5794
111 5EW9 5VC 0.03443 0.44077 5.5794
112 1XK9 P34 0.006289 0.43885 5.5814
113 3B82 NAD 0.01427 0.42223 5.7971
114 4CE5 PDG 0.002284 0.46991 6.00858
115 1JG3 ADN 0.0135 0.42084 6.00858
116 4YC0 5OF 0.01596 0.41995 6.00858
117 5DX1 SFG 0.03924 0.40033 6.00858
118 5DX8 SFG 0.03454 0.40022 6.00858
119 2VPY MGD 0.04962 0.42503 6.15385
120 1Q0S SAH 0.02071 0.41288 6.43777
121 4M73 SAH 0.04096 0.41187 6.43777
122 2X5D PLP 0.01231 0.40306 6.43777
123 4C4A SAH 0.02791 0.40139 6.43777
124 4KM2 ATR 0.0427 0.40525 6.70391
125 4KM2 TOP 0.04475 0.40525 6.70391
126 1O9J NAD 0.01444 0.42619 6.86695
127 1S4M LUM 0.02736 0.41484 6.86695
128 3LCC SAH 0.01939 0.40436 6.86695
129 1QPR PPC 0.02453 0.40073 6.86695
130 5LLT DND 0.03433 0.41454 7.04225
131 4M20 COA 0.03599 0.40135 7.08661
132 3EFV NAD 0.006698 0.44416 7.29614
133 3UZO PLP 0.006484 0.42839 7.29614
134 3QFS NAP 0.03738 0.41935 7.29614
135 3QFS FAD 0.03738 0.41935 7.29614
136 2X65 M1P 0.008207 0.41411 7.29614
137 3UZO GLU 0.02499 0.4127 7.29614
138 5LRT ADP 0.02999 0.40504 7.29614
139 4MZQ 1VU 0.02599 0.40114 7.63889
140 2JHF NAD 0.04515 0.4505 7.72532
141 1WDK NAD 0.009177 0.43337 7.72532
142 5KF6 NAD 0.03708 0.40608 7.72532
143 5LYH 7B8 0.03474 0.40353 7.77202
144 4Z9D NAD 0.02482 0.40414 8
145 5FA8 SAM 0.01131 0.42862 8.07453
146 2I0D MUT 0.03271 0.43449 8.08081
147 5F7J ADE 0.0000004854 0.65725 8.15451
148 1O97 FAD 0.01903 0.43995 8.15451
149 1O97 AMP 0.01903 0.43995 8.15451
150 1O94 AMP 0.004604 0.43457 8.15451
151 5JJU AMP 0.01369 0.40911 8.15451
152 4PZ2 NAD 0.03049 0.40863 8.15451
153 5JXZ ISJ 0.01425 0.40815 8.15451
154 5JXZ ISC 0.01549 0.40815 8.15451
155 5JY4 ISC 0.01691 0.40512 8.15451
156 4A34 FUL 0.007926 0.41579 8.16327
157 4DE9 VTP 0.005681 0.44988 8.58369
158 3NZK C90 0.006638 0.43295 8.58369
159 2WU6 DKI 0.007497 0.43223 9.01288
160 3DUW SAH 0.009608 0.42767 9.41704
161 4KRI SAH 0.01392 0.41835 9.44206
162 3RHJ NAP 0.03893 0.40839 9.44206
163 4WCX MET 0.0131 0.40374 9.44206
164 1TLG GAL 0.01259 0.40306 9.6
165 4FK7 P34 0.002732 0.40776 9.60699
166 4XUC 43G 0.009704 0.44322 10.0917
167 4XUC SAM 0.009704 0.44322 10.0917
168 3FZG SAM 0.01586 0.41051 10.5
169 1K3T BRZ 0.01822 0.43019 10.7296
170 4I8P NAD 0.01493 0.43009 11.1588
171 3OH3 UAD 0.01852 0.41772 11.1588
172 1JAY NAP 0.02358 0.40236 11.3208
173 2A5F NAD 0.01455 0.41133 11.399
174 3G2O SAM 0.02731 0.40072 11.588
175 4GLJ RHB 0.04818 0.42736 12.0172
176 1N07 ADP 0.0187 0.41226 12.2699
177 1N07 FMN 0.03461 0.41226 12.2699
178 5HPY GDP 0.02758 0.40113 12.4324
179 3EUF BAU 0.000001706 0.61683 12.4464
180 4L2I FAD 0.01179 0.43426 12.4464
181 4L2I NAD 0.01658 0.43426 12.4464
182 4FXQ G9L 0.009455 0.40888 12.4464
183 5GM1 SAH 0.03284 0.40538 12.4464
184 4XSH NAI 0.02371 0.40932 12.8492
185 4RPL 3UC 0.03656 0.43159 12.8755
186 3P0F BAU 0.007265 0.45595 13.7339
187 5ECP ATP 0.04069 0.41194 13.7339
188 5ECP JAA 0.04902 0.40666 13.7339
189 5ECP MET 0.04902 0.40666 13.7339
190 2G37 FAD 0.03086 0.40054 13.7339
191 3LF0 ATP 0.00103 0.47877 14.0351
192 5U98 1KX 0.0343 0.42698 14.1414
193 4X6F 3XU 0.01904 0.43082 14.2857
194 5F7N NAG GAL FUC FUC A2G 0.008348 0.43336 15.4506
195 5F7Y GLC GAL NAG GAL FUC A2G 0.005183 0.42788 15.4506
196 1ERB ETR 0.0116 0.42752 15.847
197 3UWV 2PG 0.02113 0.40754 16.309
198 3KVY URA 0.000000355 0.63167 16.7382
199 3KVY R2B 0.001803 0.44895 16.7382
200 5KOK SAH 0.0126 0.42118 17.1674
201 2A8Y MTA 0.000001029 0.64109 18.0258
202 4II2 ATP 0.01543 0.42092 18.0723
203 1C3X 8IG 0.000003876 0.55267 18.4549
204 4TXJ THM 0.000003927 0.62838 18.8841
205 3BJE URA 0.00000001359 0.69678 24.0343
206 3LGS ADE 0.00000001955 0.72429 32.618
207 3LGS SAH 0.00000001955 0.72429 32.618
208 3BL6 FMC 0.0007993 0.51614 33.0472
209 4BMX ADE 0.00000002369 0.72408 35.1931
210 1ZOS MTM 0.00000001334 0.72958 37.3913
211 4WKB TDI 0.00000006775 0.7024 38.1974
212 1U1F 183 0.00002985 0.59892 39.0558
213 3QPB URA 0.00000242 0.58637 40.7725
214 4YJK URA 0.0000004161 0.59771 43.7768
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