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Receptor
PDB id Resolution Class Description Source Keywords
4K7O 1.98 Å NON-ENZYME: OTHER HUMAN PEROXIREDOXIN 5 WITH A FRAGMENT HOMO SAPIENS ENZYME CYTOSOL OXIDOREDUCTASE
Ref.: COMPARING BINDING MODES OF ANALOGOUS FRAGMENTS USIN FRAGMENT-BASED DRUG DESIGN: APPLICATION TO PRDX5 PLOS ONE V. 9 02300 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS C:201;
B:202;
A:202;
B:203;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
EKZ C:202;
B:201;
A:201;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 50 uM
166.217 C10 H14 O2 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K7O 1.98 Å NON-ENZYME: OTHER HUMAN PEROXIREDOXIN 5 WITH A FRAGMENT HOMO SAPIENS ENZYME CYTOSOL OXIDOREDUCTASE
Ref.: COMPARING BINDING MODES OF ANALOGOUS FRAGMENTS USIN FRAGMENT-BASED DRUG DESIGN: APPLICATION TO PRDX5 PLOS ONE V. 9 02300 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 1HD2 - BEZ C7 H6 O2 c1ccc(cc1)....
2 4K7N Kd = 330 uM MCT C7 H8 O2 Cc1ccc(c(c....
3 4K7I Kd = 1500 uM CAQ C6 H6 O2 c1ccc(c(c1....
4 1OC3 - BEZ C7 H6 O2 c1ccc(cc1)....
5 4MMM Kd = 150 uM BP7 C12 H10 O2 c1ccc(cc1)....
6 1H4O - BEZ C7 H6 O2 c1ccc(cc1)....
7 4K7O Kd = 50 uM EKZ C10 H14 O2 CC(C)(C)c1....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 1HD2 - BEZ C7 H6 O2 c1ccc(cc1)....
2 4K7N Kd = 330 uM MCT C7 H8 O2 Cc1ccc(c(c....
3 4K7I Kd = 1500 uM CAQ C6 H6 O2 c1ccc(c(c1....
4 1OC3 - BEZ C7 H6 O2 c1ccc(cc1)....
5 4MMM Kd = 150 uM BP7 C12 H10 O2 c1ccc(cc1)....
6 1H4O - BEZ C7 H6 O2 c1ccc(cc1)....
7 4K7O Kd = 50 uM EKZ C10 H14 O2 CC(C)(C)c1....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 1HD2 - BEZ C7 H6 O2 c1ccc(cc1)....
2 4K7N Kd = 330 uM MCT C7 H8 O2 Cc1ccc(c(c....
3 4K7I Kd = 1500 uM CAQ C6 H6 O2 c1ccc(c(c1....
4 1OC3 - BEZ C7 H6 O2 c1ccc(cc1)....
5 4MMM Kd = 150 uM BP7 C12 H10 O2 c1ccc(cc1)....
6 1H4O - BEZ C7 H6 O2 c1ccc(cc1)....
7 4K7O Kd = 50 uM EKZ C10 H14 O2 CC(C)(C)c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EKZ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 EKZ 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: 188
This union binding pocket(no: 1) in the query (biounit: 4k7o.bio5) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 2GJ3 FAD None
2 4WW8 VD9 None
3 1OVD ORO 1.78571
4 1OVD FMN 1.78571
5 4KQ6 DLZ 1.78571
6 1ZUI SKM 1.78571
7 4P6W MOF 2.38095
8 5L7G 6QE 2.38095
9 5LPG 71V 2.43902
10 2F59 INI 2.54777
11 2ZGY GDP 2.8125
12 3ZY6 GFB 2.97619
13 1SQA UI1 2.97619
14 3C3N FMN 2.97619
15 2Y6P CTP 2.97619
16 3K8D CTP 2.97619
17 1G94 DAF GLC DAF GLC GLC 2.97619
18 5DQ8 FLF 2.97619
19 1S7G NAD 2.97619
20 4QYS PLP SEP 2.97619
21 5DX3 EST 2.97619
22 2QA8 GEN 2.97619
23 4MG7 27H 2.97619
24 5NDF LU2 2.97619
25 5HYR EST 2.97619
26 5WGQ EST 2.97619
27 2QZO KN1 2.97619
28 5WGD EST 2.97619
29 5NDF UDP 2.97619
30 5DXG EST 2.97619
31 4WGF HX2 2.97619
32 1BC5 SAH 2.97619
33 1ORR CDP 2.97619
34 1KYV RBF 3.14465
35 4WZH FMN 3.17003
36 1IK4 PGH 3.28947
37 4XF6 INS 3.57143
38 4XF6 LIP 3.57143
39 4XF6 ADP 3.57143
40 3Q9N COA 3.57143
41 5EK3 5PK 3.57143
42 1U3R 338 3.57143
43 1ZOA 140 3.57143
44 2YJD YJD 3.57143
45 2FFU UDP 3.57143
46 5KZD RCJ 3.57143
47 3BL6 FMC 3.57143
48 1YYE 196 3.57143
49 4R6W SAH 3.57143
50 4Q9M FPP 3.57143
51 4Q9M 2ZW 3.57143
52 1RVV INI 3.8961
53 5KY3 GFB 4.16667
54 5XFV FMN 4.16667
55 5L4S NAP 4.16667
56 5L4S 6KX 4.16667
57 6CLV 6MB 4.16667
58 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 4.16667
59 4N65 AQN 4.16667
60 5KY9 GDP 4.16667
61 5KXQ GDP 4.16667
62 3A76 SPD 4.16667
63 4GA6 AMP 4.16667
64 2WSB NAD 4.16667
65 2OQ2 A3P 4.16667
66 5N6C NAD 4.16667
67 4N65 FMN 4.16667
68 1UPF URF 4.16667
69 6ENO BJ8 4.16667
70 6CQF F97 4.7619
71 1W78 PD8 4.7619
72 4LZJ 22H 4.7619
73 4C5N ACP 4.7619
74 4C5N PXL 4.7619
75 1RLZ NAD 4.7619
76 3NNT DQA 4.7619
77 3CX8 GSP 4.7619
78 3HPY MCT 4.7619
79 1EJB INJ 4.7619
80 1FLR FLU 4.7619
81 5Y8L NAD 5.08475
82 2B99 RDL 5.12821
83 5UXH GFB 5.35714
84 1T36 U 5.35714
85 1RE8 BD2 5.35714
86 4PVV HO4 5.35714
87 3LGS SAH 5.35714
88 3LGS ADE 5.35714
89 4PFT MAB 5.35714
90 1J0X NAD 5.35714
91 1EE0 CAA 5.35714
92 4GVS F4M 5.35714
93 4TL6 ANP 5.35714
94 5GVR LMR 5.35714
95 2IYA UDP 5.35714
96 3IIJ ADP 5.35714
97 5GM9 CBK 5.35714
98 3TYZ PAB 5.35714
99 3TYZ XHP 5.35714
100 2D7C GTP 5.38922
101 16PK BIS 5.95238
102 5TDF 7A3 5.95238
103 1EP2 FMN 5.95238
104 3ND6 ATP 5.95238
105 1Q0S SAH 5.95238
106 4F9C 0SX 5.95238
107 1JBW TMF 5.95238
108 3CQD ATP 5.95238
109 1RRV TYD 5.95238
110 2C94 TSF 6.25
111 3QBT GNP 6.42857
112 3OIX FMN 6.54762
113 6FDF SAH 6.54762
114 4EU7 CIT 6.54762
115 5MZY 8EZ 6.54762
116 3OBK PBG 6.54762
117 3KV8 FAH 6.54762
118 4Z0H NAD 6.54762
119 1H9G COA MYR 6.58436
120 5UFS 1TA 7.14286
121 1RYI GOA 7.14286
122 5EEH P9P 7.14286
123 1DSS NAD 7.14286
124 1KQN NAD 7.14286
125 1RYI FAD 7.14286
126 4A22 TD4 7.14286
127 4E2J MOF 7.14286
128 4IMG NGF 7.14286
129 5ND5 TPP 7.14286
130 1XON PIL 7.14286
131 5LU5 M7P 7.14286
132 5AAV GW5 7.7381
133 2R5N RP5 7.7381
134 6ADI 9UO 7.7381
135 2VWT PYR 7.7381
136 2GKS ADP 7.7381
137 2IGA XXP 8.33333
138 2IGA XX3 8.33333
139 3A1C ACP 8.33333
140 1F1V DHY 8.92857
141 2VYN NAD 8.92857
142 3KDU NKS 8.92857
143 5J5R 6G1 8.92857
144 5J5R IMP 8.92857
145 4D8N 0HM 8.92857
146 4OKZ 3E9 8.92857
147 2DT5 NAD 8.92857
148 2EC9 24X 9.16667
149 1DQS NAD 9.52381
150 3GYT DL4 9.52381
151 3FV1 DYH 9.52381
152 2BR6 HSL 9.52381
153 5KY5 GDP 10
154 5CJH 522 10.119
155 4UTW RFW 10.119
156 2H29 DND 10.119
157 4X6F 3XU 10.4762
158 2WOE AR6 10.7023
159 4ZAL 4LR 10.7143
160 4ZAL FNR 10.7143
161 3V1Y NAD 10.7143
162 5X93 K87 10.7143
163 2Y5S 78H 10.7143
164 1RKX NAD 11.3095
165 3RWO GDP 11.3095
166 4IO2 GLU 11.3095
167 3OCP CMP 11.5108
168 5ECP MET 11.9048
169 5ECP JAA 11.9048
170 5KJZ PCG 12.5
171 5N0O SAM 12.5
172 1NE6 SP1 12.5
173 4WKC BIG 13.0612
174 5ODQ 9SB 13.0952
175 6HOY AR6 13.0952
176 3MJY IJZ 13.6905
177 3MJY FMN 13.6905
178 5KY4 GDP 15
179 4CVN ADP 15.3285
180 5UAV NDP 16.0714
181 5UAV TFB 16.0714
182 1F06 NDP 17.2619
183 5UY8 AMZ 17.8571
184 4WKB TDI 17.8571
185 3KFC 61X 20.2381
186 1PVN MZP 21.4286
187 2V2G BEZ 24.4048
188 3W6G FLC 39.2857
Pocket No.: 2; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: 90
This union binding pocket(no: 2) in the query (biounit: 4k7o.bio5) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2QBU SAH None
2 1Z08 GNP None
3 5EYG NAP None
4 1SR7 MOF 1.19048
5 4UHF BUA 1.78571
6 4J7U NAP 1.78571
7 4J7U YTZ 1.78571
8 6BMS PLM 1.78571
9 1T0A FPP 1.88679
10 4P6X HCY 2.38095
11 1ZHX HC3 2.38095
12 4AVB ACO 2.38095
13 4P53 NAI 2.38095
14 1GJC 130 2.97619
15 1WMA NDP 2.97619
16 1WMA AB3 2.97619
17 1KZN CBN 2.97619
18 3UUD EST 2.97619
19 1N5D NDP 2.97619
20 5DXE EST 2.97619
21 4LY9 1YY 2.97619
22 4LY9 S6P 2.97619
23 4X1T UDP 2.97619
24 2P3B 3TL 3.0303
25 2P3C 3TL 3.0303
26 2I0G I0G 3.57143
27 4J26 EST 3.57143
28 3WCA FPS 3.57143
29 4RDZ MYR 3.57143
30 2WKW W22 3.57143
31 5O98 NAP 3.57143
32 3OLL EST 3.57143
33 4OHB 5HM 3.57143
34 4JEM C5P 3.57143
35 4A4X JUP 4.16667
36 3G5N PB2 4.7619
37 3NC9 TR3 4.7619
38 1GTE FAD 4.7619
39 2PI8 NAG NAG NAG NAG NAG NAG 4.7619
40 4N02 FNR 4.7619
41 4YBN FAD 4.7619
42 4G6I RS3 4.7619
43 5BO9 SIA GAL NGS 4.7619
44 1XUJ BOZ 5.35714
45 4XVU ATP 5.35714
46 1OIX GDP 5.35714
47 1U7Z PMT 5.35714
48 1TKB N1T 5.35714
49 2PZI AXX 5.35714
50 2BCG GDP 5.95238
51 2R5V HHH 5.95238
52 1EP2 ORO 5.95238
53 3CIF NAD 5.95238
54 3CIF G3H 5.95238
55 1F74 NAY 6.54762
56 6CFC BLG 6.54762
57 3NEM AMO 6.54762
58 4GBM A3P 6.54762
59 1J0D 5PA 7.14286
60 1A2C 34H LEU PRJ OAR 7.7381
61 6FX0 E9T 7.7381
62 5QB1 F1C 7.7381
63 4XTR ATP 8.10811
64 4XTR ADP 8.10811
65 2IGA XX2 8.33333
66 3NJ4 AFX 8.33333
67 3KA2 2NC 8.86699
68 1GR0 NAD 8.92857
69 2HV8 GTP 8.92857
70 4C4P GNP 9.34579
71 1IUP ALQ 9.52381
72 2CWH PYC 9.52381
73 1BZY IMU 10.119
74 5CMK GLU 10.7143
75 1XKD NAP 11.3095
76 4AVO BGC BGC BGC BGC BGC BGC 11.3095
77 3WBF API 11.3095
78 5A8R TP7 11.9048
79 1NVM NAD 11.9048
80 3AWJ COA 11.9048
81 1ELU CSS 11.9048
82 2X3F APC 13.0952
83 3RDE OYP 13.0952
84 1P31 EPU 13.6905
85 3NUG NAD 13.6905
86 6AYR BIG 14.2857
87 3RS8 APR 16.6667
88 5Z2F NAP 16.6667
89 3ZOK NAD 19.0476
90 5Z84 PSC 22.9358
Pocket No.: 3; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: 73
This union binding pocket(no: 3) in the query (biounit: 4k7o.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3GWL FAD None
2 4Q9N 0WE None
3 3R1V AZB None
4 3D78 NBB None
5 3FSM 2NC 1.78571
6 1UVC STE 2.1978
7 6CEP NAD 2.38095
8 6CEP OXM 2.38095
9 3BZ3 YAM 2.38095
10 3CB2 GDP 2.38095
11 4UDB CV7 2.38095
12 3G5S FAD 2.97619
13 4ZVI 4S4 2.97619
14 6C6O ENG 3.57143
15 3P2H NOO 3.57143
16 1NF8 ISC 3.57143
17 2B4R AES 3.57143
18 2B4R NAD 3.57143
19 4DPL NAP 4.16667
20 5KOR GDP 4.16667
21 3R77 QLI 4.16667
22 2QDT I38 4.16667
23 3VDB 149 4.16667
24 3MTW M3R 4.16667
25 2I6U CP 4.16667
26 4SGA ACE PRO ALA PRO PHE 4.16667
27 5W8Q BU4 4.7619
28 3VZS CAA 4.7619
29 4V24 GYR 4.7619
30 3IP8 B85 4.7619
31 5DF1 NAP 4.7619
32 5DF1 58X 4.7619
33 6AP8 BNY 4.7619
34 5A89 FMN 5.12821
35 5A89 ADP 5.12821
36 5NXX 3Q7 5.35714
37 3NTY 5P3 5.35714
38 1E2K TMC 5.35714
39 3TK1 GDP 5.35714
40 3ZGJ RMN 5.35714
41 3I54 CMP 5.35714
42 3COW 52H 5.35714
43 1PIG AGL GLC HMC AGL GLC BGC 5.35714
44 5C1M 4VO 5.6
45 3E1T FAD 5.95238
46 6AMI TRP 5.95238
47 5NQR 958 5.95238
48 3SQG TP7 5.95238
49 4UCI GTP 5.95238
50 2D3M COA 5.95238
51 6CUZ FEV 6.54762
52 4WPF 3SN 6.54762
53 4EIL NDP 6.54762
54 4NBU CAA 7.14286
55 1FCZ 156 7.7381
56 4LC1 GDP 8.92857
57 3ZOA ACR 8.92857
58 3EYA TDP 10.119
59 1H65 GDP 10.7143
60 5N1Q TP7 11.3095
61 1FMB HYB 12.5
62 5KBF CMP 12.5
63 1F2U ATP 12.7517
64 5FJN BE2 13.0952
65 3ZG6 APR 13.0952
66 4KBY C2E 13.0952
67 9LDB NAD 14.881
68 2O4C NAD 15.4762
69 1C4Q GLA GAL BGC 15.942
70 3I8P 840 17.8571
71 1IDA 0PO 18.1818
72 5ZCO PSC 22.9358
73 5FAW CHT 28.5714
Pocket No.: 4; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: 7
This union binding pocket(no: 4) in the query (biounit: 4k7o.bio4) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1XSE NDP 2.97619
2 4O4K 2PK 2.97619
3 4GLL NAD 3.57143
4 1JBW ACQ 5.95238
5 5FFF NAP 8.33333
6 1LLU NAD 11.3095
7 4G4S LDZ 23.2143
Pocket No.: 5; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4k7o.bio4) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: 66
This union binding pocket(no: 6) in the query (biounit: 4k7o.bio3) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1OGX EQU None
2 3IBH GSH 1.19048
3 1LDN NAD 1.78571
4 2V2V V12 1.78571
5 3QP8 HL0 1.78571
6 3SIX GDP 2.38095
7 4TUZ 36J 2.97619
8 4MG8 27J 2.97619
9 4NE2 SH2 2.97619
10 4NE2 ADP 2.97619
11 2BJ4 OHT 2.97619
12 4MGD 27N 2.97619
13 4MGB XDH 2.97619
14 5W19 9TD 2.97619
15 4EN4 GT0 3.57143
16 4EN4 GT1 3.57143
17 4EN4 ATP 3.57143
18 6C8X BVR 4.0404
19 3HNC TTP 4.16667
20 3BEO UDP 4.16667
21 2RL1 UD1 4.16667
22 5ENZ UDP 4.16667
23 1RPN NDP 4.7619
24 5BO9 CSF 4.7619
25 1KUV CA5 5.35714
26 1CJW COT 5.35714
27 1T36 ADP 5.35714
28 4ZRN NAD 5.35714
29 2UXR ICT 5.35714
30 3FQ8 PMP 5.35714
31 3KJD 78P 5.95238
32 4S28 SAH 5.95238
33 4S28 AIR 5.95238
34 4AF0 IMP 6.54762
35 5V03 658 6.71141
36 4RSL FAD 7.14286
37 6APL C5P 7.14286
38 5I39 FAD 7.7381
39 3VCY UD1 7.7381
40 1F6D UDP 7.7381
41 2ZCQ B65 7.7381
42 4GID 0GH 7.7381
43 5T2Z 017 8.08081
44 2YAJ 4HP 8.33333
45 4Q5M ROC 8.92857
46 1V8B ADN 8.92857
47 3H9E NAD 8.92857
48 2HJR APR 8.92857
49 4IRX INS 10.119
50 4PTZ FMN 10.7143
51 4P5E N6P 11.1842
52 6CI9 NAP 11.3095
53 5U97 PIT 11.3095
54 1NWW HPN 11.4094
55 5EXE 5SR 12.5
56 1GOT GDP 13.0952
57 3NZW BOC TY5 ALA RE0 ABN 14.881
58 4NES UDP 16.0714
59 1F06 2NP 17.2619
60 4L9Z COA 17.2619
61 1MLY ACZ PLP 18.4524
62 2XCG XCG 19.0476
63 4DEC UDP 19.0476
64 4DEC 3PG 19.0476
65 2DYS PSC 22.9358
66 6C28 WCA 25.5952
Pocket No.: 7; Query (leader) PDB : 4K7O; Ligand: EKZ; Similar sites found with APoc: 24
This union binding pocket(no: 7) in the query (biounit: 4k7o.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5WQP NAP 1.78571
2 5UUO GSH 1.78571
3 5ZI2 NAD 2.38095
4 5AJP UDP 2.97619
5 1OAA OAA 3.57143
6 2DT9 THR 3.59281
7 2YC5 6BC 4.16667
8 3HY3 10F 4.7619
9 3VZS NAP 4.7619
10 3A2Q ACA ACA 4.7619
11 3NTY NAP 5.35714
12 2OOR TXP 6.54762
13 5W10 CMP 6.54762
14 1CT9 AMP 6.54762
15 3NRR D16 7.14286
16 2R5N R5P 7.7381
17 2VVT DGL 8.33333
18 3VSV XYS 8.33333
19 5NTW 98N 9.52381
20 4OYA 1VE 11.3095
21 3B1Q NOS 11.3095
22 1VBI NAD 11.3095
23 3CAQ NDP 13.0952
24 9LDT NAD 14.881
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