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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
6F4W 2.29 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF H. PYLORI PURINE NUCLEOSIDE PHOSPHORYLA COMPLEX WITH FORMYCIN A HELICOBACTER PYLORI PURINE NUCLEOSIDE PHOSPHORYLASE H. PYLORI FORMYCIN A HYDR
Ref.: HELICOBACTER PYLORI PURINE NUCLEOSIDE PHOSPHORYLASE NEW DISTRIBUTION PATTERNS OF OPEN AND CLOSED ACTIVE CONFORMATIONS AND UNUSUAL BIOCHEMICAL FEATURES. FEBS J. V. 285 1305 2018
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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(....
4 6F4X Kd = 10.7 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
5 6F4W Kd = 2.95 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
70% Homology Family (39)
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 6F4X Kd = 10.7 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
27 6F4W Kd = 2.95 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
28 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
29 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
30 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
32 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
33 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
34 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
35 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
36 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
37 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
38 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
39 4DAB - HPA C5 H4 N4 O c1[nH]c2c(....
50% Homology Family (45)
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 6F4X Kd = 10.7 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
27 6F4W Kd = 2.95 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
28 1JDT - MTA C11 H15 N5 O3 S CSC[C@@H]1....
29 1JE1 - GMP C10 H13 N5 O5 c1nc2c(n1[....
30 1JDZ - FMB C10 H12 N4 O5 C1=Nc2c(n[....
31 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
32 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
33 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
34 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
35 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
36 1ODI Kd = 62 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
37 1ODJ Kd = 80 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
38 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
39 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
40 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
41 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
42 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
43 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
44 4DAB - HPA C5 H4 N4 O c1[nH]c2c(....
45 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 : 6F4W; Ligand: FMC; Similar sites found with APoc: 113
This union binding pocket(no: 1) in the query (biounit: 6f4w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5HWV MBN None
2 5F6U 5VK None
3 3QXV MTX None
4 3A16 PXO 1.71674
5 1ELI PYC 2.14592
6 4PXL NAD 2.14592
7 1I2L DCS 2.14592
8 1TPY SAH 2.14592
9 3VZS CAA 2.57511
10 5K3W PLP 2.57511
11 1JV1 UD1 2.57511
12 5IUW IAC 2.57511
13 3VC1 GST 2.57511
14 3VC1 SAH 2.57511
15 1JGT APC 2.57511
16 1JGT CMA 2.57511
17 1KPH SAH 2.57511
18 2A9K NAD 2.69058
19 5DYO FLU 2.83019
20 1OJZ NAD 2.83019
21 1GZF NAD 2.8436
22 1GZF ADP 2.8436
23 4ITH RCM 3.00429
24 5EWK P34 3.00429
25 2BZG SAH 3.01724
26 4MA7 P2Z 3.28639
27 1KDK DHT 3.38983
28 1K27 MTM 3.43348
29 5W75 SUC 3.43348
30 5WS9 OXL 3.43348
31 3LVW GSH 3.43348
32 5U3F 7TS 3.86266
33 1GPM AMP 3.86266
34 1RJW ETF 3.86266
35 1WG8 SAM 3.86266
36 2C5S AMP 3.86266
37 1VKF CIT 4.25532
38 2UUU PL3 4.29185
39 4QAR ADE 4.47761
40 6ACS CIT 4.72103
41 3BGD PM6 4.72103
42 3BGD SAH 4.72103
43 2WN6 NDP 4.72103
44 2XXP DSL 4.72103
45 2G2Y MLI 4.72103
46 5UAV NDP 4.72103
47 4PNE SAH 4.72103
48 2ZMF CMP 4.7619
49 1IYE PGU 5.15021
50 3G6K FAD 5.15021
51 3G6K POP 5.15021
52 3ESS 18N 5.21739
53 1RC0 KT5 5.26316
54 4GLJ RHB 5.5794
55 4UUG PXG 5.5794
56 1XK9 P34 5.5814
57 3B82 NAD 5.7971
58 4B2Z P5S 6.00858
59 4CE5 PDG 6.00858
60 6B5G CQY 6.00858
61 2YLN CYS 6.00858
62 2G50 PYR 6.43777
63 2QV7 ADP 6.43777
64 2BJK NAD 6.86695
65 5I60 67W 7.29614
66 3DAA PDD 7.29614
67 4YRY NAD 7.29614
68 5DX0 SFG 7.29614
69 5DX1 SFG 7.29614
70 3HQP OXL 7.72532
71 1RM0 NAI 7.72532
72 2R5N R5P 7.72532
73 2R5N RP5 7.72532
74 2R5N TPP 7.72532
75 5F7J ADE 8.15451
76 3HRD NIO 8.15451
77 5YSI NCA 8.55263
78 4FK7 P34 9.60699
79 2XG5 EC5 9.82659
80 2XG5 EC2 9.82659
81 4L2I NAD 10.1156
82 2A5F NAD 11.9171
83 3EUF BAU 12.4464
84 4PIO SAH 12.4464
85 5GM1 SAH 12.4464
86 4PIO AVI 12.4464
87 5FPX GLY SER SER HIS HIS HIS HIS HIS 13.2743
88 3P0F BAU 13.7339
89 3LF0 ATP 14.0351
90 1USF NAP 14.6067
91 1USF FMN 14.6067
92 2BVE PH5 15.126
93 3KVY R2B 16.7382
94 3KVY URA 16.7382
95 1YB5 NAP 18.0258
96 1C3X 8IG 18.4549
97 4TXJ THM 18.8841
98 2A8Y MTA 18.8841
99 3BJE URA 24.0343
100 3BJE R1P 24.0343
101 3LGS ADE 26.6094
102 3LGS SAH 26.6094
103 6AYR BIG 33.9056
104 4BMX ADE 35.1931
105 4WKC BIG 36.0515
106 3BL6 FMC 36.9565
107 1ZOS MTM 36.9565
108 4FFS BIG 37.2385
109 4WKB TDI 38.1974
110 1U1F 183 39.0558
111 3QPB R1P 40.3433
112 3QPB URA 40.3433
113 4YJK URA 43.7768
Pocket No.: 2; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 21
This union binding pocket(no: 2) in the query (biounit: 6f4w.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2WSI FAD 2.14592
2 5XDT MB3 2.14592
3 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 2.57511
4 5IUW NAD 2.57511
5 4OYA 1VE 3.00429
6 3VZ3 NAP 3.43348
7 4S00 AKR 3.86266
8 6EK3 OUL 4.0724
9 4R38 RBF 4.28571
10 3FIU AMP 4.29185
11 1MDC PLM 4.54545
12 1F0X FAD 5.15021
13 5YJS SAL 5.5794
14 2VPY MGD 6.15385
15 1QPR PPC 6.86695
16 3RHJ NAP 9.44206
17 1TLG GAL 9.6
18 4IPE ANP 10.7296
19 4I8P NAD 11.1588
20 2IV2 2MD 11.588
21 4FXQ G9L 12.4464
Pocket No.: 3; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 9
This union binding pocket(no: 3) in the query (biounit: 6f4w.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1GZF NIR 2.8436
2 5KJW 53C 3.43348
3 1T9D FAD 3.86266
4 1PZG A3D 4.72103
5 6B5G NAD 6.00858
6 3K5I AIR 6.86695
7 3FPF MTA 12.8755
8 3FPF TNA 12.8755
9 4YHQ G10 13.1313
Pocket No.: 4; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 12
This union binding pocket(no: 4) in the query (biounit: 6f4w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 6B2M COA 2.57511
2 1EXF GLY 3.00429
3 1XNG ATP 3.00429
4 3DLG GWE 3.00429
5 5M3E APR 3.63636
6 6GNO XDI 3.7037
7 2YQS UD1 4.29185
8 3IWK NAD 4.72103
9 3OZ2 FAD 5.03778
10 3KJD 78P 6.43777
11 1GQ2 NAP 9.01288
12 4WCX MET 9.44206
Pocket No.: 5; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 14
This union binding pocket(no: 5) in the query (biounit: 6f4w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5E72 SAM 2.14592
2 4NEC SAH 2.57511
3 1KPG SAH 2.57511
4 4PLT NAI 3.00429
5 4PLT OXM 3.00429
6 1GQG DCD 3.43348
7 4A0M NAD 3.43348
8 3EYA FAD 4.29185
9 3HNB 768 6.28931
10 1Q0S SAH 6.43777
11 4BTI 7R9 6.43777
12 1TKB N1T 6.43777
13 5A89 FMN 7.05128
14 3C2O NTM 13.7339
Pocket No.: 6; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 3
This union binding pocket(no: 6) in the query (biounit: 6f4w.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2WDB NAG MAN 1.5625
2 2J5S KTA 2.57511
3 2ATJ BHO 4.29185
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