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: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 DAL FAD PER 0.772414 0.951807
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 62F 0.572327 0.939024
12 F2N 0.566265 0.886364
13 FMN 0.543307 0.876543
14 FA9 0.526316 0.939759
15 6YU 0.516304 0.860215
16 CNV FAD 0.511905 0.908046
17 P6G FDA 0.511628 0.908046
18 FAD NBT 0.508876 0.83871
19 A2D 0.504065 0.875
20 P5F 0.491329 0.941176
21 FAD CNX 0.488506 0.8125
22 APR 0.488372 0.851852
23 AR6 0.488372 0.851852
24 AGS 0.484615 0.811765
25 SAP 0.484615 0.811765
26 M33 0.484375 0.864198
27 BA3 0.484127 0.875
28 FAD NBA 0.480663 0.802083
29 ATP 0.48062 0.851852
30 B4P 0.480315 0.875
31 ADP 0.480315 0.851852
32 AP5 0.480315 0.875
33 ANP 0.477273 0.831325
34 AQP 0.476923 0.851852
35 5FA 0.476923 0.851852
36 48N 0.469388 0.902439
37 OAD 0.467626 0.876543
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AD9 0.462121 0.831325
41 3OD 0.460993 0.876543
42 RBF 0.460938 0.790123
43 FB0 0.460606 0.835165
44 139 0.460526 0.858824
45 AP0 0.46 0.835294
46 A22 0.459854 0.864198
47 ACP 0.458015 0.853659
48 8QN 0.456522 0.864198
49 PRX 0.454545 0.831325
50 A1R 0.453237 0.86747
51 G3A 0.452055 0.902439
52 T5A 0.45098 0.872093
53 G5P 0.44898 0.902439
54 ATF 0.448529 0.821429
55 50T 0.44697 0.819277
56 ACQ 0.444444 0.853659
57 PAJ 0.442857 0.847059
58 ADQ 0.442857 0.853659
59 5AL 0.441176 0.864198
60 ADX 0.439394 0.775281
61 CA0 0.439394 0.853659
62 A4P 0.437909 0.831461
63 25L 0.4375 0.864198
64 P33 FDA 0.436464 0.817204
65 5SV 0.435714 0.793103
66 TXE 0.434211 0.890244
67 OMR 0.434211 0.818182
68 ABM 0.434109 0.829268
69 A 0.433071 0.82716
70 AMP 0.433071 0.82716
71 4AD 0.432624 0.855422
72 ADJ 0.432258 0.818182
73 BIS 0.430556 0.802326
74 SRA 0.429688 0.788235
75 AFH 0.42953 0.825581
76 TXD 0.427632 0.890244
77 NXX 0.427632 0.865854
78 UP5 0.427632 0.878049
79 DND 0.427632 0.865854
80 6V0 0.427632 0.857143
81 SRP 0.42446 0.843373
82 PR8 0.423611 0.837209
83 TAT 0.423358 0.821429
84 AMO 0.422535 0.865854
85 PTJ 0.42069 0.835294
86 FYA 0.42069 0.864198
87 TXA 0.42069 0.865854
88 CNA 0.420382 0.865854
89 00A 0.41958 0.823529
90 AHX 0.41958 0.835294
91 MAP 0.41844 0.811765
92 NAI 0.418301 0.845238
93 AU1 0.41791 0.831325
94 AP2 0.416667 0.843373
95 A12 0.416667 0.843373
96 25A 0.415493 0.851852
97 AMP MG 0.415385 0.785714
98 COD 0.415094 0.842697
99 ADP BEF 0.414815 0.77907
100 BEF ADP 0.414815 0.77907
101 4TC 0.412903 0.879518
102 APC 0.411765 0.843373
103 NB8 0.410959 0.835294
104 ME8 0.410959 0.806818
105 1ZZ 0.410959 0.806818
106 4UW 0.409091 0.825581
107 NAX 0.409091 0.837209
108 RBY 0.408759 0.843373
109 ADV 0.408759 0.843373
110 ADP MG 0.407407 0.797619
111 P1H 0.405882 0.818182
112 OOB 0.405594 0.864198
113 A A 0.40411 0.829268
114 LAD 0.40411 0.825581
115 UPA 0.403846 0.86747
116 4UU 0.401316 0.833333
117 A3D 0.401235 0.876543
118 DLL 0.4 0.864198
119 XAH 0.4 0.806818
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: 29
This union binding pocket(no: 1) in the query (biounit: 4h6q.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RL4 PPV 0.01924 0.42039 1.41509
2 1SDW IYT 0.01062 0.41635 1.60256
3 1RHC F42 ACN 0.002193 0.41836 2.5641
4 4RW3 IPD 0.006057 0.43721 2.64901
5 5W3Y ACO 0.01729 0.4168 2.88462
6 5BRP PNG 0.0049 0.44992 3.20513
7 3NZ1 3NY 0.02056 0.40894 3.83142
8 2YMZ LAT 0.02499 0.40473 3.84615
9 3P7G MAN 0.04153 0.40021 4.10959
10 5L9G MO0 0.01363 0.40383 4.48718
11 3APT FAD 0.0005997 0.4291 4.51613
12 3FGC FMN 0.0001306 0.44069 5.44872
13 5DG2 GAL GLC 0.02718 0.40309 5.92593
14 3OQJ 3CX 0.01465 0.41344 7.00389
15 5H9O GLC 0.02408 0.41289 7.05128
16 5CPR 539 0.02965 0.40186 7.08955
17 2G50 PYR 0.005729 0.43505 7.69231
18 4X8D AVI 0.02266 0.40991 8.33333
19 4NAE 1GP 0.01165 0.42732 9.77778
20 1UJP CIT 0.01142 0.40399 10.3321
21 5A07 GDP 0.02529 0.40156 10.5769
22 5W3X ACO 0.02988 0.40621 11.25
23 1ZPT FAD 0.005444 0.41178 15.1316
24 4O8A FAD 0.00000000001651 0.74856 42.6282
25 3HAZ FAD 0.0000000002305 0.70222 44.5513
26 5KF6 TFB 0.0000000000115 0.76042 45.8333
27 5KF6 FAD 0.0000000000115 0.76042 45.8333
28 4NMC 2OP 0.00000000001096 0.76895 49.0385
29 4NMC FAD 0.00000000001253 0.76895 49.0385
Pocket No.: 2; Query (leader) PDB : 4H6Q; Ligand: TFB; Similar sites found: 42
This union binding pocket(no: 2) in the query (biounit: 4h6q.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RL4 PPV 0.0224 0.42039 1.41509
2 3WV6 GAL BGC 0.03176 0.40355 1.68919
3 1RHC F42 ACN 0.002714 0.40635 2.5641
4 4RW3 PLM 0.01515 0.44241 2.64901
5 4RW3 IPD 0.006685 0.43926 2.64901
6 4RW3 TDA 0.03592 0.40962 2.64901
7 5BRP PNG 0.005892 0.44963 3.20513
8 5V4R MGT 0.009213 0.44382 3.7037
9 5ABU GTG 0.02038 0.41863 3.80435
10 3NZ1 3NY 0.02403 0.40894 3.83142
11 2YMZ LAT 0.03035 0.40389 3.84615
12 5UGW GSH 0.03611 0.40382 4
13 5FQK 6NT 0.0401 0.4037 4.46097
14 5L9G MO0 0.01535 0.40544 4.48718
15 3APT FAD 0.0008384 0.4305 4.51613
16 4UCC ZKW 0.019 0.41124 5.15021
17 3FGC FMN 0.0001907 0.4197 5.44872
18 3E3U NVC 0.01828 0.40524 5.58376
19 5DG2 GAL GLC 0.03368 0.40121 5.92593
20 3OQJ 3CX 0.0176 0.41344 7.00389
21 5H9O GLC 0.0251 0.41568 7.05128
22 2G50 PYR 0.006796 0.43505 7.69231
23 3G5K BB2 0.008301 0.42178 8.19672
24 4X8D AVI 0.0262 0.40991 8.33333
25 5EXA 5SO 0.02015 0.41444 9.56522
26 4NAE 1GP 0.01377 0.42732 9.77778
27 1UJP CIT 0.003852 0.42984 10.3321
28 5A07 GDP 0.02953 0.40202 10.5769
29 5OCA 9QZ 0.01876 0.40983 11.0599
30 2Y69 CHD 0.01363 0.42471 11.1111
31 2VWA PTY 0.02534 0.41575 11.8812
32 4YMU ARG 0.0475 0.40062 15
33 1ZPT FAD 0.004674 0.40674 15.1316
34 1WS1 BB2 0.01092 0.41243 16.0256
35 5CHR 4NC 0.01032 0.43591 17.5182
36 3RV5 DXC 0.01256 0.47217 19.1011
37 4O8A FAD 0.00000000008934 0.69535 42.6282
38 3HAZ FAD 0.000000001084 0.65369 44.5513
39 5KF6 TFB 0.0000000000007273 0.78158 45.8333
40 5KF6 FAD 0.0000000000007273 0.78158 45.8333
41 4NMC 2OP 0.0000000000007985 0.78824 49.0385
42 4NMC FAD 0.0000000000009291 0.78824 49.0385
Pocket No.: 3; Query (leader) PDB : 4H6Q; Ligand: FAD; Similar sites found: 5
This union binding pocket(no: 3) in the query (biounit: 4h6q.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G6K POP 0.006541 0.40561 1.94805
2 1V6A TRE 0.03477 0.40161 2.88462
3 4A91 GLU 0.003873 0.45538 3.02013
4 5ABU GTG 0.01838 0.41619 3.80435
5 1O68 KIV 0.01823 0.41562 6.90909
Pocket No.: 4; Query (leader) PDB : 4H6Q; Ligand: TFB; Similar sites found: 15
This union binding pocket(no: 4) in the query (biounit: 4h6q.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2YIP YIO 0.04789 0.40473 None
2 1SDW IYT 0.01052 0.41796 1.60256
3 4CNO 9PY 0.02628 0.41147 1.98413
4 1XM4 PIL 0.02331 0.40103 2.24359
5 3R9V DXC 0.03436 0.40472 2.44755
6 1V6A TRE 0.0389 0.40161 2.88462
7 4A91 GLU 0.004151 0.45617 3.02013
8 5HSS 650 0.01826 0.41406 3.52564
9 3P7G MAN 0.04314 0.40051 4.10959
10 4WOE ADP 0.04022 0.40223 5.12821
11 1RZM E4P 0.0333 0.40287 5.76923
12 1O68 KIV 0.01991 0.41639 6.90909
13 4YMJ 4EJ 0.02743 0.41029 8.22368
14 1PVN MZP 0.006175 0.40791 8.65385
15 4O8A 2OP 0.000000007666 0.40889 42.6282
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