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Receptor
PDB id Resolution Class Description Source Keywords
4H6Q 1.36 Å EC: 1.5.99.8 STRUCTURE OF OXIDIZED DEINOCOCCUS RADIODURANS PROLINE DEHYDR COMPLEXED WITH L-TETRAHYDROFUROIC ACID DEINOCOCCUS RADIODURANS BETA8-ALPHA8-BARREL FLAVOENZYME OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES AND KINETICS OF MONOFUNCTIONAL P DEHYDROGENASE PROVIDE INSIGHT INTO SUBSTRATE RECOGN CONFORMATIONAL CHANGES ASSOCIATED WITH FLAVIN REDUC PRODUCT RELEASE. BIOCHEMISTRY V. 51 10099 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:2001;
C:2001;
 Valid;
Valid;
 none;
none;
 submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
GOL A:2003;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
TFB A:2002;
C:2002;
 Valid;
Valid;
 none;
none;
 Ki = 38 mM
116.115 C5 H8 O3 C1C[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4H6Q 1.36 Å EC: 1.5.99.8 STRUCTURE OF OXIDIZED DEINOCOCCUS RADIODURANS PROLINE DEHYDR COMPLEXED WITH L-TETRAHYDROFUROIC ACID DEINOCOCCUS RADIODURANS BETA8-ALPHA8-BARREL FLAVOENZYME OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES AND KINETICS OF MONOFUNCTIONAL P DEHYDROGENASE PROVIDE INSIGHT INTO SUBSTRATE RECOGN CONFORMATIONAL CHANGES ASSOCIATED WITH FLAVIN REDUC PRODUCT RELEASE. BIOCHEMISTRY V. 51 10099 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4H6Q Ki = 38 mM TFB C5 H8 O3 C1C[C@H](O....
2 4H6R - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4H6Q Ki = 38 mM TFB C5 H8 O3 C1C[C@H](O....
2 4H6R - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2G37 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5M42 Kd = 19.5 nM FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 4H6Q Ki = 38 mM TFB C5 H8 O3 C1C[C@H](O....
4 4H6R - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 FAD 1 1
2 FAS 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 FAE 0.751773 0.987654
7 SFD 0.651007 0.860215
8 FDA 0.641892 0.906977
9 FNK 0.602564 0.876405
10 62F 0.572327 0.939024
11 F2N 0.566265 0.886364
12 FMN 0.543307 0.876543
13 FA9 0.526316 0.939759
14 6YU 0.516304 0.860215
15 P6G FDA 0.511628 0.908046
16 FAD NBT 0.508876 0.83871
17 A2D 0.504065 0.875
18 P5F 0.491329 0.941176
19 FAD CNX 0.488506 0.8125
20 AR6 0.488372 0.851852
21 APR 0.488372 0.851852
22 AGS 0.484615 0.811765
23 SAP 0.484615 0.811765
24 M33 0.484375 0.864198
25 BA3 0.484127 0.875
26 HEJ 0.48062 0.851852
27 ATP 0.48062 0.851852
28 ADP 0.480315 0.851852
29 B4P 0.480315 0.875
30 AP5 0.480315 0.875
31 ANP 0.477273 0.831325
32 AQP 0.476923 0.851852
33 5FA 0.476923 0.851852
34 48N 0.469388 0.902439
35 OAD 0.467626 0.876543
36 9X8 0.467626 0.833333
37 FAD NBA 0.467033 0.793814
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AT4 0.465116 0.821429
41 AD9 0.462121 0.831325
42 3OD 0.460993 0.876543
43 RBF 0.460938 0.790123
44 FB0 0.460606 0.835165
45 139 0.460526 0.858824
46 AP0 0.46 0.835294
47 A22 0.459854 0.864198
48 ACP 0.458015 0.853659
49 8QN 0.456522 0.864198
50 PRX 0.454545 0.831325
51 A3R 0.453237 0.86747
52 A1R 0.453237 0.86747
53 G3A 0.452055 0.902439
54 T5A 0.45098 0.872093
55 G5P 0.44898 0.902439
56 ATF 0.448529 0.821429
57 50T 0.44697 0.819277
58 6YZ 0.445255 0.853659
59 ACQ 0.444444 0.853659
60 CNV FAD 0.443182 0.917647
61 ADQ 0.442857 0.853659
62 PAJ 0.442857 0.847059
63 5AL 0.441176 0.864198
64 ADX 0.439394 0.775281
65 CA0 0.439394 0.853659
66 A4P 0.437909 0.831461
67 25L 0.4375 0.864198
68 P33 FDA 0.436464 0.817204
69 5SV 0.435714 0.793103
70 OMR 0.434211 0.818182
71 TXE 0.434211 0.890244
72 ABM 0.434109 0.829268
73 A 0.433071 0.82716
74 AMP 0.433071 0.82716
75 4AD 0.432624 0.855422
76 ADJ 0.432258 0.818182
77 B5M 0.431507 0.878049
78 B5Y 0.431507 0.878049
79 BIS 0.430556 0.802326
80 SRA 0.429688 0.788235
81 AFH 0.42953 0.825581
82 NXX 0.427632 0.865854
83 DND 0.427632 0.865854
84 UP5 0.427632 0.878049
85 6V0 0.427632 0.857143
86 TXD 0.427632 0.890244
87 DQV 0.426667 0.8875
88 SRP 0.42446 0.843373
89 PR8 0.423611 0.837209
90 T99 0.423358 0.821429
91 TAT 0.423358 0.821429
92 AMO 0.422535 0.865854
93 TXA 0.42069 0.865854
94 FYA 0.42069 0.864198
95 PTJ 0.42069 0.835294
96 CNA 0.420382 0.865854
97 00A 0.41958 0.823529
98 AHX 0.41958 0.835294
99 MAP 0.41844 0.811765
100 NAI 0.418301 0.845238
101 AU1 0.41791 0.831325
102 A12 0.416667 0.843373
103 AP2 0.416667 0.843373
104 25A 0.415493 0.851852
105 9ZA 0.415493 0.845238
106 9ZD 0.415493 0.845238
107 COD 0.415094 0.842697
108 4TC 0.412903 0.879518
109 APC 0.411765 0.843373
110 ME8 0.410959 0.806818
111 1ZZ 0.410959 0.806818
112 NB8 0.410959 0.835294
113 4UW 0.409091 0.825581
114 NAX 0.409091 0.837209
115 F2R 0.408805 0.850575
116 RBY 0.408759 0.843373
117 ADV 0.408759 0.843373
118 P1H 0.405882 0.818182
119 OOB 0.405594 0.864198
120 LAD 0.40411 0.825581
121 A A 0.40411 0.829268
122 UPA 0.403846 0.86747
123 4UU 0.401316 0.833333
124 GA7 0.401316 0.865854
125 A3D 0.401235 0.876543
126 80F 0.401235 0.808989
127 XAH 0.4 0.806818
128 DLL 0.4 0.864198
Ligand no: 2; Ligand: TFB; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 TFB 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4H6Q; Ligand: FAD; Similar sites found with APoc: 103
This union binding pocket(no: 1) in the query (biounit: 4h6q.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 6BKK 308 None
2 5CLO NS8 None
3 2YIP YIO None
4 2BOS GLA GAL GLC None
5 5KZD RCJ 0.682594
6 5HGZ MLA 1.23457
7 3GJB AKG 1.28205
8 6FNU FAD 1.2987
9 4RL4 PPV 1.41509
10 1M3U KPL 1.51515
11 1SDW IYT 1.60256
12 1UH4 GLC 1.60256
13 4YZ5 SLT 1.60256
14 4I9A NCN 2.08333
15 6GNO XDI 2.22222
16 4BS0 6NT 2.24359
17 4IP7 FLC 2.5641
18 1RHC F42 ACN 2.5641
19 6DAW ARG 2.5641
20 3RLF MAL 2.5641
21 5YJS SAL 2.5641
22 3A23 GAL 2.5641
23 4RW3 IPD 2.64901
24 1Y7P RIP 2.69058
25 5W3Y ACO 2.88462
26 3U6W KIV 2.88462
27 5BRP PNG 3.20513
28 6FCX FAD 3.20513
29 2ZZV LAC 3.20513
30 6BSX E7S 3.37079
31 3EGI ADP 3.39806
32 5C8W PCG 3.4965
33 5KJW 53C 3.52564
34 1F9V ADP 3.52564
35 5L2R MLA 3.52564
36 1ONI BEZ 3.62319
37 3DUV KDO 3.81679
38 3NZ1 3NY 3.83142
39 2XN2 GLA 3.84615
40 2YMZ LAT 3.84615
41 3P7G MAN 4.10959
42 6FBA D48 4.16667
43 3U1T MLI 4.20712
44 4CQB MLI 4.25532
45 1VKF CIT 4.25532
46 3KDM TES 4.44444
47 1KTC NGA 4.48718
48 1FDJ 13P 4.48718
49 5L9G MO0 4.48718
50 3APT FAD 4.51613
51 3B4Y F42 4.80769
52 5WAN FMN 4.80769
53 1AX2 NDG GAL 5.02092
54 2J9D AMP 5.04202
55 5WS9 OXL 5.12821
56 1ZGS XMM 5.12821
57 5X7Q GLC GLC GLC GLC 5.12821
58 5WS9 ATP 5.12821
59 3QH2 3NM 5.42986
60 3FGC FMN 5.44872
61 4B3J COA 5.44872
62 5AHO TLA 5.76923
63 3H55 GLA 5.76923
64 4NFE BEN 5.90717
65 5UIJ TYD 5.92593
66 5DG2 GAL GLC 5.92593
67 4KCT PYR 6.41026
68 2W68 SIA GAL BGC 6.66667
69 1O68 KIV 6.90909
70 3OQJ 3CX 7.00389
71 5H9O GLC 7.05128
72 3EF0 ALF 7.05128
73 2BGM MAX 7.05128
74 4NZF ARB 7.05128
75 3MKK GLC BGC 7.05128
76 5CPR 539 7.08955
77 2G50 PYR 7.69231
78 4X8D AVI 8.33333
79 5EXK MET 8.33333
80 4FFG LBS 8.65385
81 3HQP OXL 8.65385
82 1UAS GLA 9.61539
83 4NAE 1GP 9.77778
84 6BT4 KPM 9.90099
85 1UJP CIT 10.3321
86 5A07 GDP 10.5769
87 2J83 BAT 10.687
88 2YFO GAL 10.8974
89 2YFO GLA 10.8974
90 4PTN GXV 11.2179
91 5W3X ACO 11.25
92 1HFE CYS 13.0081
93 5W97 CHD 13.2653
94 1ZPT FAD 15.1316
95 1QPR PHT 19.0141
96 3FGZ BEF 22.6562
97 4O8A FAD 42.6282
98 4O8A 2OP 42.6282
99 3HAZ FAD 44.5513
100 5KF6 FAD 45.8333
101 5KF6 TFB 45.8333
102 4NMC FAD 49.0385
103 4NMC 2OP 49.0385
Pocket No.: 2; Query (leader) PDB : 4H6Q; Ligand: TFB; Similar sites found with APoc: 190
This union binding pocket(no: 2) in the query (biounit: 4h6q.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5TVI O8N None
2 1UO5 PIH None
3 2YIP YIO None
4 4WG0 CHD None
5 5CLO NS8 None
6 2FKA BEF None
7 4F4S EFO None
8 6BKK 308 None
9 6E2B PT7 None
10 2BOS GLA GAL GLC None
11 5KZD RCJ 0.682594
12 5HGZ MLA 1.23457
13 3GJB AKG 1.28205
14 6FNU FAD 1.2987
15 3VWX GSH 1.35135
16 4RL4 PPV 1.41509
17 1M3U KPL 1.51515
18 1UH4 GLC 1.60256
19 2RH1 CAU 1.60256
20 5DXT 5H5 1.60256
21 4YZ5 SLT 1.60256
22 1M5W DXP 1.64609
23 3WV6 GAL BGC 1.68919
24 5OLK DTP 1.92308
25 5IM3 DTP 1.92308
26 4I9A NCN 2.08333
27 6GNO XDI 2.22222
28 1XMY ROL 2.24359
29 4BS0 6NT 2.24359
30 5L7V GNL 2.24359
31 3B6O TMP 2.42915
32 4WGF HX2 2.43902
33 3RLF MAL 2.5641
34 4IP7 FLC 2.5641
35 1S20 TLA 2.5641
36 1RHC F42 ACN 2.5641
37 6DAW ARG 2.5641
38 3JSX CC2 2.5641
39 5YJS SAL 2.5641
40 3NB0 G6P 2.5641
41 3JQQ A2P 2.5641
42 2F7A BEZ 2.58621
43 4DR9 BB2 2.60417
44 4RW3 PLM 2.64901
45 4RW3 IPD 2.64901
46 4RW3 TDA 2.64901
47 1Y7P RIP 2.69058
48 1SR9 KIV 2.88462
49 3U6W KIV 2.88462
50 4V3I ASP LEU THR ARG PRO 3.11284
51 5XJD 87L 3.18182
52 5BRP PNG 3.20513
53 6FCX FAD 3.20513
54 2XN3 ID8 3.20513
55 2ZZV LAC 3.20513
56 1C9K 5GP 3.33333
57 2GWH PCI 3.3557
58 6BSX E7S 3.37079
59 3EGI ADP 3.39806
60 3N8K D1X 3.48837
61 5C8W PCG 3.4965
62 5KJW 53C 3.52564
63 1F9V ADP 3.52564
64 5HSS 650 3.52564
65 5LY1 PPI 3.52564
66 1ONI BEZ 3.62319
67 3AQT RCO 3.67347
68 5V4R MGT 3.7037
69 3M3E GAL A2G NPO 3.72671
70 1K12 FUC 3.79747
71 5ABU GTG 3.80435
72 3DUV KDO 3.81679
73 3NZ1 3NY 3.83142
74 2XN2 GLA 3.84615
75 4MRP GSH 3.84615
76 6MVU K4V 3.84615
77 2YMZ LAT 3.84615
78 4D1J DGJ 3.84615
79 6BR8 PGV 3.96825
80 5UGW GSH 4
81 6FBA D48 4.16667
82 1B4B ARG 4.22535
83 6CI9 F3V 4.2471
84 1VKF CIT 4.25532
85 4RHP PEF 4.25532
86 3KDM TES 4.44444
87 5FQK 6NT 4.46097
88 1KTC NGA 4.48718
89 1FDJ 13P 4.48718
90 2YAJ 4HP 4.48718
91 5L9G MO0 4.48718
92 3APT FAD 4.51613
93 3P9T TCL 4.56621
94 4JE7 BB2 4.56853
95 5Y02 HBX 4.6729
96 5WAN FMN 4.80769
97 2ZID GLC GLC GLC 4.80769
98 3B4Y F42 4.80769
99 5W7B MYR 4.96454
100 2J9D AMP 5.04202
101 5WS9 OXL 5.12821
102 4D52 GXL 5.12821
103 4UCC ZKW 5.15021
104 1DEK DGP 5.39419
105 3QH2 3NM 5.42986
106 3FGC FMN 5.44872
107 3E3U NVC 5.58376
108 5FH7 5XL 5.64516
109 5AHO TLA 5.76923
110 3H55 GLA 5.76923
111 4NFE BEN 5.90717
112 5UIJ TYD 5.92593
113 5DG2 GAL GLC 5.92593
114 4TQK NAG 6.08974
115 4KCT PYR 6.41026
116 3O01 DXC 6.49351
117 2HHP FLC 6.73077
118 5MDH MAK 6.73077
119 1RQH PYR 6.73077
120 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.80272
121 1O68 KIV 6.90909
122 3OQJ 3CX 7.00389
123 5H9O GLC 7.05128
124 4NZF ARB 7.05128
125 3EF0 ALF 7.05128
126 6BXO SAH 7.05128
127 2BGM MAX 7.05128
128 3MKK GLC BGC 7.05128
129 2BP1 FLC 7.05128
130 5EHS 2JJ 7.46269
131 5EHS 5OY 7.46269
132 2G50 PYR 7.69231
133 5LX9 OLB 7.74648
134 6CAM BGC 8.01282
135 4F06 PHB 8.01282
136 5V3Y 5V8 8.04196
137 3G5K BB2 8.19672
138 4UTW RFW 8.29694
139 4X8D AVI 8.33333
140 5EXK MET 8.33333
141 4TV1 36M 8.36653
142 4FFG LBS 8.65385
143 3EPO MP5 8.65385
144 3HQP OXL 8.65385
145 2EFE GNH 8.83978
146 4EKQ NPO 9.09091
147 5EXA 5SO 9.56522
148 5M36 9SZ 9.60699
149 1UAS GLA 9.61539
150 4NAE 1GP 9.77778
151 6BT4 KPM 9.90099
152 2D6M LBT 10.0629
153 4OGQ 7PH 10.2326
154 1UJP CIT 10.3321
155 1P6O HPY 10.559
156 5A07 GDP 10.5769
157 2J83 BAT 10.687
158 2YFO GAL 10.8974
159 2YFO GLA 10.8974
160 5OCA 9QZ 11.0599
161 2Y69 CHD 11.1111
162 4PTN GXV 11.2179
163 5MWE TCE 11.4286
164 2VWA PTY 11.8812
165 3KP6 SAL 11.9205
166 4RJD TFP 12.1212
167 3UN3 G16 12.5
168 3CH6 311 12.5874
169 3CH6 NAP 12.5874
170 5ZCO CHD 13.2653
171 5Z84 CHD 13.2653
172 5W97 CHD 13.2653
173 5ZCO PGV 13.2653
174 4YMU ARG 15
175 1ZPT FAD 15.1316
176 5C9J DAO 15.1515
177 4C01 QY9 15.6028
178 1WS1 BB2 16.0256
179 1VR0 3SL 16.5992
180 5CHR 4NC 17.5182
181 1QPR PHT 19.0141
182 3RV5 DXC 19.1011
183 3FGZ BEF 22.6562
184 4O8A 2OP 42.6282
185 4O8A FAD 42.6282
186 3HAZ FAD 44.5513
187 5KF6 FAD 45.8333
188 5KF6 TFB 45.8333
189 4NMC FAD 49.0385
190 4NMC 2OP 49.0385
Pocket No.: 3; Query (leader) PDB : 4H6Q; Ligand: FAD; Similar sites found with APoc: 17
This union binding pocket(no: 3) in the query (biounit: 4h6q.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4Z7X 3CX 0.840336
2 3E5P PPI 1.92308
3 4CLO XP0 2.08333
4 2YVK MRU 2.40642
5 3FSY SCA 2.5641
6 6CLV 6MB 2.74914
7 1V6A TRE 2.88462
8 3R7F CP 2.96053
9 4A91 GLU 3.02013
10 5ABU GTG 3.80435
11 6E1Q CFA 3.84615
12 5T9C G3P 4.10448
13 6BXO SAH 7.05128
14 1XVB BHL 7.05882
15 5EHS 5OY 7.46269
16 5EHS 2JJ 7.46269
17 3C8E GSH 7.98611
Pocket No.: 4; Query (leader) PDB : 4H6Q; Ligand: TFB; Similar sites found with APoc: 34
This union binding pocket(no: 4) in the query (biounit: 4h6q.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 4Z7X 3CX 0.840336
2 4OCT AKG 1.35135
3 1SDW IYT 1.60256
4 4CNO 9PY 1.98413
5 1XM4 PIL 2.24359
6 2YVK MRU 2.40642
7 3R9V DXC 2.44755
8 3FSY SCA 2.5641
9 2OZ5 7XY 2.7027
10 1R6N 434 2.8436
11 1V6A TRE 2.88462
12 3R7F CP 2.96053
13 4A91 GLU 3.02013
14 4DVE BTN 3.0303
15 4JGX PLM 3.10078
16 5HSS 64Z 3.52564
17 5L2R MLA 3.52564
18 1JW0 GUA 3.79747
19 6E1Q CFA 3.84615
20 2ZQO NGA 3.84615
21 4U0S ADP 3.84615
22 3P7G MAN 4.10959
23 1AX2 NDG GAL 5.02092
24 4WOE ADP 5.12821
25 4D52 GIV 5.12821
26 1RZM E4P 5.76923
27 1XVB BHL 7.05882
28 5YW0 SIN 7.37179
29 5CMK LY5 7.72201
30 4YMJ 4EJ 8.22368
31 1PVN MZP 8.65385
32 4XCB AKG 8.81226
33 5Z84 PGV 13.2653
34 2DYR PGV 13.2653
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