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Receptor
PDB id Resolution Class Description Source Keywords
5EXE 1.88 Å EC: 1.2.7.10 CRYSTAL STRUCTURE OF OXALATE OXIDOREDUCTASE FROM MOORELLA THERMOACETICA BOUND WITH CARBOXY-TPP ADDUCT MOORELLA THERMOACETICA (STRAIN ATCC 39ORGANISM_TAXID: 264732 OXALATE OXIDOREDUCTASE OFOR THIAMINE
Ref.: ONE-CARBON CHEMISTRY OF OXALATE OXIDOREDUCTASE CAPT X-RAY CRYSTALLOGRAPHY. PROC.NATL.ACAD.SCI.USA V. 113 320 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA F:404;
Part of Protein;
none;
submit data
22.99 Na [Na+]
SF4 E:401;
B:401;
C:401;
F:401;
B:402;
E:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
MG F:403;
C:404;
C:403;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
5SR F:402;
C:402;
Valid;
Valid;
none;
none;
submit data
468.316 C13 H18 N4 O9 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EXE 1.88 Å EC: 1.2.7.10 CRYSTAL STRUCTURE OF OXALATE OXIDOREDUCTASE FROM MOORELLA THERMOACETICA BOUND WITH CARBOXY-TPP ADDUCT MOORELLA THERMOACETICA (STRAIN ATCC 39ORGANISM_TAXID: 264732 OXALATE OXIDOREDUCTASE OFOR THIAMINE
Ref.: ONE-CARBON CHEMISTRY OF OXALATE OXIDOREDUCTASE CAPT X-RAY CRYSTALLOGRAPHY. PROC.NATL.ACAD.SCI.USA V. 113 320 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5EXD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5C4I - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 5EXE - 5SR C13 H18 N4 O9 P2 S Cc1c(sc([n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5EXD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5C4I - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 5EXE - 5SR C13 H18 N4 O9 P2 S Cc1c(sc([n....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5EXD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5C4I - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 5EXE - 5SR C13 H18 N4 O9 P2 S Cc1c(sc([n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5SR; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 5SR 1 1
2 O2T 0.711111 0.935065
3 HTL 0.709302 0.959459
4 TDP 0.582418 0.958333
5 TDL 0.57732 0.923077
6 TOG 0.565657 0.947368
7 TDW 0.56383 0.945946
8 AUJ 0.556701 0.922078
9 TD6 0.554455 0.947368
10 THV 0.546392 0.933333
11 TD9 0.543689 0.947368
12 TD8 0.543689 0.947368
13 WWF 0.540816 0.909091
14 THY 0.535354 0.921053
15 THW 0.529412 0.933333
16 TDK 0.524752 0.897436
17 8PA 0.5 0.921053
18 D7K 0.490909 0.886076
19 TPP 0.479167 0.945205
20 T6F 0.477477 0.875
21 T5X 0.477477 0.875
22 V4E 0.474747 0.945205
23 TMV 0.44 0.906667
24 PYI 0.434343 0.837838
25 TPW 0.43299 0.849315
26 R1T 0.431373 0.837838
27 S1T 0.431373 0.837838
28 TPS 0.421053 0.90411
29 1U0 0.419048 0.794872
30 TPU 0.408163 0.797468
31 N1T 0.401961 0.958333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EXE; Ligand: 5SR; Similar sites found with APoc: 165
This union binding pocket(no: 1) in the query (biounit: 5exe.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2X1L MET 3.03797
2 4MOB ADP 3.1746
3 3ITJ CIT 3.18471
4 5UXF 2BA 3.49206
5 2IHT TPP 3.5443
6 2IHU TP9 3.5443
7 1UPA TPP 3.5443
8 1M0S CIT 3.65297
9 2IYA UDP 3.79747
10 2J4D MHF 3.79747
11 5ND5 TPP 3.82166
12 1N4K I3P 4.14013
13 4PPF FLC 4.14013
14 4YKI GLY 4.29688
15 1Z6K OAA 4.43686
16 3IAE D7K 4.44444
17 2UZ1 TPP 4.44444
18 1R9J TPP 4.4586
19 5T8U LPA 4.4586
20 4XFR CIT 4.55696
21 3KCC CMP 4.61538
22 1PFK ADP 4.6875
23 3WMX THR 4.7486
24 5MB4 NAG 4.7619
25 3DRW AMP 4.7619
26 3A06 NDP 4.77707
27 6APL C5P 4.81283
28 2WD7 VGD 4.85075
29 5LQ8 GB 4.96454
30 3DVA TPW 5.06329
31 4HSE ADP 5.07937
32 2OEM 1AE 5.07937
33 2R5N TPP 5.09554
34 2R5N RP5 5.09554
35 2R5N R5P 5.09554
36 1KJ8 GAR 5.11509
37 1JG0 DDT 5.30303
38 4UP4 GAL NAG 5.31646
39 3OTH TYD 5.41401
40 3MBC NAP 5.56962
41 4O48 ASP 5.71429
42 3KFL ME8 5.73248
43 1WUU GLA 5.76441
44 3QDK QDK 5.82278
45 3KV5 OGA 5.82278
46 1ZPD DPX 6.03175
47 2WPW ACO 6.03175
48 2WPX ACO 6.03175
49 4A91 GLU 6.04027
50 1SJD NPG 6.05096
51 2YPI PGA 6.07287
52 4TWL ASC 6.09756
53 5W6Y TRP 6.32911
54 1R6B ADP 6.32911
55 1RRV TYD 6.32911
56 3KC1 2T6 6.34921
57 4KGD FAD 6.36943
58 4KGD TDP 6.36943
59 2XZ9 PYR 6.36943
60 1SQ5 PAU 6.49351
61 3I7S PYR 6.50685
62 1QS0 TDP 6.58228
63 5WKC TP9 6.6879
64 5WKC AUJ 6.6879
65 1T9D P25 6.6879
66 1T9D FAD 6.6879
67 1T9D 1MM 6.6879
68 1T9D PYD 6.6879
69 5VRH OLB 6.6879
70 1T9D P22 6.6879
71 3NOJ PYR 6.72269
72 1YBH P22 6.83544
73 1KSK URA 6.83761
74 3W6G FLC 6.94444
75 3EYA TDP 6.98413
76 4DE3 DN8 7.22433
77 4DDY DN6 7.22433
78 4UAA 3GK 7.22433
79 5GLN XYP XYP XYP 7.26744
80 5XET ME8 7.32484
81 5AIP 4HP 7.53425
82 2O1S TDP 7.59494
83 1TKB N1T 7.59494
84 4D5G TPP 7.61905
85 4D5G FAD 7.61905
86 1KC7 PPR 7.61905
87 2VBF TPP 7.64331
88 2XDQ MGX 7.64331
89 2WCV FUC 7.85714
90 3HWW AKG 7.93651
91 1PFY MSP 7.93651
92 1Q19 SSC 7.96178
93 5D2H AKG 8.12721
94 2BO4 FLC 8.25397
95 1OZH HE3 8.28025
96 5B0I BOG 8.45481
97 3FSJ D7K 8.57143
98 1V5F FAD 8.59873
99 1V5F TPP 8.59873
100 1RP7 TZD 8.59873
101 5UC9 MYR 8.84956
102 1UMD TDP COI 8.9172
103 5TSH ADP 8.9172
104 4RDN 6MD 8.98204
105 2X7I CIT 9.09091
106 5A96 GTP 9.23695
107 2CHT TSA 9.44882
108 4EHQ GBL 9.45946
109 5ESO ISC 9.52381
110 5ESO TDP 9.52381
111 5V49 MET 9.55414
112 4KVL PLM 9.84127
113 3BY8 MLT 9.85915
114 5V6F MAN BMA MAN 10.1449
115 1ITZ TPP 10.3797
116 4CCK OGA 10.4762
117 3A16 PXO 10.5096
118 2IYF UDP 10.7937
119 4TQK NAG 10.7937
120 2J9D ADP 10.9244
121 2J9D AMP 10.9244
122 5NM7 GLY 11.1111
123 2NV2 GLN 11.1111
124 2VK4 TPP 11.1465
125 6DEN TP9 11.1465
126 6DEN G8A 11.1465
127 6DEN FAD 11.1465
128 2X7J TPP 11.4286
129 1OLS TDP 11.7834
130 5AMH EF2 12
131 5WHU SIA 12.0805
132 1QPB PYM 12.1019
133 1QPB TPP 12.1019
134 4K7O EKZ 12.5
135 1A8U BEZ 12.6354
136 2NXW TPP 12.9114
137 1V3S ATP 12.931
138 3AI7 TPP 13.1646
139 4QXB OGA 13.2353
140 1I7Q BEZ 13.3333
141 5G48 1FL 13.3758
142 2GNK ATP 13.3929
143 4RJK TPP 13.6709
144 4RJK TDL 13.6709
145 3PMA SCR 13.7931
146 3EXH TPP 13.9683
147 2OZL TPP 13.9683
148 4USI ATP 14.9351
149 3NCQ ATP 15.126
150 3PH4 AOS 15.3846
151 4ZV1 ARG 18.0258
152 1P4V GLY 18.7302
153 2C31 ADP 18.7302
154 2C31 TZD 18.7302
155 1APZ ASP 19.8582
156 3TA2 AKG 21.1864
157 4F4S EFO 22.3684
158 4PU6 ASP 24.4275
159 5B48 TDN 24.918
160 5B47 PYR 25.9868
161 5B47 TPP 25.9868
162 1W85 TDP 30.6122
163 2C42 TPP 35.443
164 2C42 PYR 35.443
165 4CCN OGA 37.1429
Pocket No.: 2; Query (leader) PDB : 5EXE; Ligand: 5SR; Similar sites found with APoc: 55
This union binding pocket(no: 2) in the query (biounit: 5exe.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 5TZ6 7OD 2.92208
2 5T96 79J 3.18471
3 5A1S FLC 3.50318
4 6F5W KG1 3.52304
5 5GQI CTP 4.8583
6 3B6O TMP 4.8583
7 3W2W ATP 4.96894
8 6A4R ASP 5.28302
9 1NCE CB3 5.30303
10 2QS8 MET 5.31646
11 5XVR TRH 5.39683
12 5O22 C3R 5.53633
13 5YXC CIT 5.55556
14 1RZM E4P 5.73248
15 4D86 ADP 5.73248
16 1UCN ADP 5.92105
17 4YUS FMN 6.03175
18 5N53 8NB 6.15385
19 2OWZ CIT 6.3253
20 5KNK 11A 6.34921
21 1UJ5 5RP 6.60793
22 4E03 ADP 6.79612
23 5TG5 JW8 6.93878
24 1GAW FAD 7.00637
25 6FXR UDP 7.00637
26 4DE2 DN3 7.22433
27 4UA7 3GK 7.22433
28 5OFW 9TW 7.30159
29 3FJG 3PG 7.56972
30 6G47 SIA SIA 7.6555
31 6CD1 PLS 7.96178
32 5H41 IFM 8.35443
33 5FS0 5JC 8.53081
34 6A46 DCM 8.59375
35 2INV FRU FRU 8.59873
36 1JOC ITP 8.8
37 5ZI9 FLC 8.84615
38 5O3Q CMP 9.16667
39 4V1F BQ1 9.30233
40 1SM4 FAD 9.7973
41 1LK7 DER 10.917
42 2QMC GTB 11.1702
43 1IK4 PGH 11.1842
44 4QVB F42 11.5646
45 4LHD GLY 11.8987
46 2CBO TH2 12.1739
47 1VAY AZA 12.1951
48 1FX8 BOG 12.8114
49 5WXK TYD 12.8571
50 1OS7 AKG 13.4276
51 1LYX PGA 13.7097
52 5J32 IPM 15.5556
53 3HEE R5P 17.4497
54 2QQC AG2 20.7547
55 2VT3 ATP 20.9302
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