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Receptor
PDB id Resolution Class Description Source Keywords
4DJA 1.45 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE PHRB FRO AGROBACTERIUM TUMEFACIENS WITH AN FE-S CLUSTER AND A 6,7-DIR IBITYLLUMAZINE ANTENNA CHROMOPHORE AT 1.45A RESOLUTION AGROBACTERIUM TUMEFACIENS PHOTOLYASE DNA REPAIR LYASE IRON-SULFUR CLUSTER FLAVOPRO
Ref.: CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE FE-S CLUSTER AND A 6,7-DIMETHYL-8-RIBITYLLUMAZINE A CHROMOPHORE. PROC.NATL.ACAD.SCI.USA V. 110 7217 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DLZ A:602;
Valid;
none;
submit data
326.305 C13 H18 N4 O6 CC1=C...
SF4 A:603;
Part of Protein;
none;
submit data
351.64 Fe4 S4 [S]12...
GOL A:606;
A:605;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA A:604;
Part of Protein;
none;
submit data
22.99 Na [Na+]
FAD A:601;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DJA 1.45 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE PHRB FRO AGROBACTERIUM TUMEFACIENS WITH AN FE-S CLUSTER AND A 6,7-DIR IBITYLLUMAZINE ANTENNA CHROMOPHORE AT 1.45A RESOLUTION AGROBACTERIUM TUMEFACIENS PHOTOLYASE DNA REPAIR LYASE IRON-SULFUR CLUSTER FLAVOPRO
Ref.: CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE FE-S CLUSTER AND A 6,7-DIMETHYL-8-RIBITYLLUMAZINE A CHROMOPHORE. PROC.NATL.ACAD.SCI.USA V. 110 7217 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 46 families.
1 5LFA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5KCM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 6DD6 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4DJA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 5LFA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5KCM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 6DD6 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4DJA - FAD C27 H33 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 35 families.
1 5LFA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5KCM - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 6DD6 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4DJA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DLZ; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 DLZ 1 1
2 1VY 0.698413 0.955882
3 RBF 0.546667 0.885714
4 RLP 0.506494 0.887324
5 RS3 0.506173 0.837838
6 FMN 0.404494 0.782051
Ligand no: 2; 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DJA; Ligand: FAD; Similar sites found with APoc: 139
This union binding pocket(no: 1) in the query (biounit: 4dja.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 5N8V KZZ None
2 4WG0 CHD None
3 1UO5 PIH None
4 1GQ2 OXL 1.1583
5 4O4Z N2O 1.2987
6 5ZM0 FAD 1.37525
7 2UW1 GVM 1.47929
8 3AQT RCO 1.73745
9 1GY8 UDP 1.76322
10 3TDC 0EU 1.9305
11 3NB0 G6P 1.9305
12 5FPN KYD 1.9305
13 5ENZ UDP 2.07792
14 1OJ4 ANP 2.12014
15 6FK6 DOK 2.14067
16 3CV3 UDP 2.21675
17 4XH0 ADP 2.23325
18 1EQ2 ADQ 2.25806
19 5N7O 69Y 2.26244
20 1ZED PNP 2.27273
21 1J1R ADE 2.29885
22 5VE5 GSH 2.38727
23 1F6D UDP 2.39362
24 2RH1 CLR 2.4
25 1J78 OLA 2.40175
26 4MRP GSH 2.443
27 2YIV YIV 2.50965
28 1WMA AB3 2.53623
29 1QB7 ADE 2.54237
30 1MZV AMP 2.55319
31 3ZJQ NCA 2.5641
32 3W68 VIV 2.63158
33 4GU5 FAD 2.7027
34 1DNP FAD 2.76008
35 4QGE 35O 2.89575
36 3BEO UDP 2.93333
37 4I90 CHT 2.9703
38 4XNV BUR 3.08789
39 2PJL 047 3.23887
40 1EXF GLY 3.30579
41 2W1A TSA 3.33333
42 2HIM ASN 3.35196
43 5U97 PIT 3.4749
44 5LX9 OLB 3.58306
45 2ZTS ADP 3.58566
46 6MVU K4V 3.66795
47 3OJI PYV 3.7037
48 5V13 JH3 3.81944
49 3UBW 6SP 3.83142
50 2HHP FLC 3.861
51 1GNI OLA 3.861
52 5ICK FEZ 3.93013
53 4DYG MES 4.09836
54 1I0B PEL 4.21687
55 3Q3H UDP 4.2471
56 3W54 RNB 4.25532
57 3W6X HZP 4.36681
58 2GEK GDP 4.4335
59 1XMY ROL 4.52261
60 1XM4 PIL 4.52261
61 1XMU ROF 4.52261
62 1QNF FAD 4.54545
63 1QNF HDF 4.54545
64 5UGW GSH 4.57143
65 1ECM TSA 4.58716
66 2UVO NDG 4.67836
67 2UVO NAG 4.67836
68 1NWW HPN 4.69799
69 3G58 988 4.72441
70 6CB2 OLC 4.77816
71 5V3Y 5V8 4.82625
72 6G5J EM8 4.84848
73 3O01 DXC 4.87013
74 1WOG 16D 4.91803
75 4UBS DIF 5.08906
76 6BR8 6OU 5.15873
77 3ZPG 5GP 5.2356
78 4G86 BNT 5.28169
79 3KP6 SAL 5.29801
80 2BCG GER 5.33981
81 3F8C HT1 5.55556
82 1DTL BEP 5.59006
83 3SQP 3J8 5.59846
84 5AZC PGT 5.66667
85 4JGT PYR 5.79151
86 5X3R 7Y3 5.85366
87 4K10 NI9 6.07735
88 5XK9 GST 6.46552
89 4XB4 45D 6.57895
90 4RKK GLC GLC GLC GLC GLC GLC 6.92771
91 3B99 U51 7.15789
92 5CHR 4NC 7.29927
93 1YNS HPO 7.66284
94 3EWK FAD 7.92952
95 1XZ3 ICF 8.04598
96 5N26 CPT 8.24176
97 2GBB CIT 8.33333
98 4DS8 A8S 8.45481
99 5A4W QCT 8.49057
100 5W7B MYR 8.51064
101 1GEG GLC 8.59375
102 4WGF HX2 9.26829
103 4V1F BQ1 9.30233
104 4CDN FAD 9.54357
105 4CDN FO1 9.54357
106 1LNX URI 9.87654
107 1MID LAP 9.89011
108 5MTE BB2 10.219
109 4MA7 P2Z 10.3286
110 3UMV FAD 10.4743
111 1RL4 BL5 10.6383
112 2QUN FUD 10.6897
113 5EQ0 5R0 PHE ALA LEU ELY 5R5 10.9091
114 2J4D FAD 11.583
115 5C1M OLC 12
116 4V3I ASP LEU THR ARG PRO 12.8405
117 5OSW DIU 15.251
118 1NU4 MLA 15.4639
119 2IDO TMP 15.6627
120 4U0S ADP 15.8301
121 2J07 FAD 15.9524
122 2J07 HDF 15.9524
123 1U3D FAD 18.2711
124 2VWA PTY 18.8119
125 2Y69 CHD 18.9189
126 5Z84 CHD 19.1781
127 5ZCO CHD 19.1781
128 5W97 CHD 19.1781
129 1P19 IMP 19.457
130 1T0S BML 19.7674
131 1N13 AG2 21.2389
132 1N8V BDD 22.3214
133 5C9J DAO 23.2323
134 1HBK MYR 24.7191
135 1HBK COA 24.7191
136 3LQV ADE 25.641
137 4OGQ 7PH 27.027
138 5M36 9SZ 28.9474
139 5NNT DPV 35.1351
Pocket No.: 2; Query (leader) PDB : 4DJA; Ligand: DLZ; Similar sites found with APoc: 139
This union binding pocket(no: 2) in the query (biounit: 4dja.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 5N8V KZZ None
2 4WG0 CHD None
3 1UO5 PIH None
4 1GQ2 OXL 1.1583
5 4O4Z N2O 1.2987
6 5ZM0 FAD 1.37525
7 2UW1 GVM 1.47929
8 3AQT RCO 1.73745
9 1GY8 UDP 1.76322
10 3TDC 0EU 1.9305
11 3NB0 G6P 1.9305
12 5FPN KYD 1.9305
13 5ENZ UDP 2.07792
14 1OJ4 ANP 2.12014
15 6FK6 DOK 2.14067
16 3CV3 UDP 2.21675
17 4XH0 ADP 2.23325
18 1EQ2 ADQ 2.25806
19 5N7O 69Y 2.26244
20 1ZED PNP 2.27273
21 1J1R ADE 2.29885
22 5VE5 GSH 2.38727
23 1F6D UDP 2.39362
24 2RH1 CLR 2.4
25 1J78 OLA 2.40175
26 4MRP GSH 2.443
27 2YIV YIV 2.50965
28 1WMA AB3 2.53623
29 1QB7 ADE 2.54237
30 1MZV AMP 2.55319
31 3ZJQ NCA 2.5641
32 3W68 VIV 2.63158
33 4GU5 FAD 2.7027
34 1DNP FAD 2.76008
35 4QGE 35O 2.89575
36 3BEO UDP 2.93333
37 4I90 CHT 2.9703
38 4XNV BUR 3.08789
39 2PJL 047 3.23887
40 1EXF GLY 3.30579
41 2W1A TSA 3.33333
42 2HIM ASN 3.35196
43 5U97 PIT 3.4749
44 5LX9 OLB 3.58306
45 2ZTS ADP 3.58566
46 6MVU K4V 3.66795
47 3OJI PYV 3.7037
48 5V13 JH3 3.81944
49 3UBW 6SP 3.83142
50 2HHP FLC 3.861
51 1GNI OLA 3.861
52 5ICK FEZ 3.93013
53 4DYG MES 4.09836
54 1I0B PEL 4.21687
55 3Q3H UDP 4.2471
56 3W54 RNB 4.25532
57 3W6X HZP 4.36681
58 2GEK GDP 4.4335
59 1XMY ROL 4.52261
60 1XM4 PIL 4.52261
61 1XMU ROF 4.52261
62 1QNF FAD 4.54545
63 1QNF HDF 4.54545
64 5UGW GSH 4.57143
65 1ECM TSA 4.58716
66 2UVO NDG 4.67836
67 2UVO NAG 4.67836
68 1NWW HPN 4.69799
69 3G58 988 4.72441
70 6CB2 OLC 4.77816
71 5V3Y 5V8 4.82625
72 6G5J EM8 4.84848
73 3O01 DXC 4.87013
74 1WOG 16D 4.91803
75 4UBS DIF 5.08906
76 6BR8 6OU 5.15873
77 3ZPG 5GP 5.2356
78 4G86 BNT 5.28169
79 3KP6 SAL 5.29801
80 2BCG GER 5.33981
81 3F8C HT1 5.55556
82 1DTL BEP 5.59006
83 3SQP 3J8 5.59846
84 5AZC PGT 5.66667
85 4JGT PYR 5.79151
86 5X3R 7Y3 5.85366
87 4K10 NI9 6.07735
88 5XK9 GST 6.46552
89 4XB4 45D 6.57895
90 4RKK GLC GLC GLC GLC GLC GLC 6.92771
91 3B99 U51 7.15789
92 5CHR 4NC 7.29927
93 1YNS HPO 7.66284
94 3EWK FAD 7.92952
95 1XZ3 ICF 8.04598
96 5N26 CPT 8.24176
97 2GBB CIT 8.33333
98 4DS8 A8S 8.45481
99 5A4W QCT 8.49057
100 5W7B MYR 8.51064
101 1GEG GLC 8.59375
102 4WGF HX2 9.26829
103 4V1F BQ1 9.30233
104 4CDN FAD 9.54357
105 4CDN FO1 9.54357
106 1LNX URI 9.87654
107 1MID LAP 9.89011
108 5MTE BB2 10.219
109 4MA7 P2Z 10.3286
110 3UMV FAD 10.4743
111 1RL4 BL5 10.6383
112 2QUN FUD 10.6897
113 5EQ0 5R0 PHE ALA LEU ELY 5R5 10.9091
114 2J4D FAD 11.583
115 5C1M OLC 12
116 4V3I ASP LEU THR ARG PRO 12.8405
117 5OSW DIU 15.251
118 1NU4 MLA 15.4639
119 2IDO TMP 15.6627
120 4U0S ADP 15.8301
121 2J07 FAD 15.9524
122 2J07 HDF 15.9524
123 1U3D FAD 18.2711
124 2VWA PTY 18.8119
125 2Y69 CHD 18.9189
126 5Z84 CHD 19.1781
127 5ZCO CHD 19.1781
128 5W97 CHD 19.1781
129 1P19 IMP 19.457
130 1T0S BML 19.7674
131 1N13 AG2 21.2389
132 1N8V BDD 22.3214
133 5C9J DAO 23.2323
134 1HBK MYR 24.7191
135 1HBK COA 24.7191
136 3LQV ADE 25.641
137 4OGQ 7PH 27.027
138 5M36 9SZ 28.9474
139 5NNT DPV 35.1351
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