Receptor
PDB id Resolution Class Description Source Keywords
3RC1 1.71 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF KIJD10, A 3-KETOREDUCTASE FROM ACTINOMA KIJANIATA INCOMPLEX WITH NADP AND TDP-BENZENE ACTINOMADURA KIJANIATA SUGAR BIOSYNTHESIS KETOREDUCTASE TDP BINDING NADP BINDINGBINDING PROTEIN
Ref.: COMBINED STRUCTURAL AND FUNCTIONAL INVESTIGATION OF C-3''-KETOREDUCTASE INVOLVED IN THE BIOSYNTHESIS OF DTDP-L-DIGITOXOSE. BIOCHEMISTRY V. 50 5905 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:338;
A:339;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
EDO A:337;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NA A:336;
Part of Protein;
none;
submit data
22.99 Na [Na+]
NAP A:335;
Valid;
none;
submit data
743.405 C21 H28 N7 O17 P3 c1cc(...
PO4 A:333;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
TLO A:334;
Valid;
none;
submit data
478.284 C16 H20 N2 O11 P2 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3RC1 1.71 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF KIJD10, A 3-KETOREDUCTASE FROM ACTINOMA KIJANIATA INCOMPLEX WITH NADP AND TDP-BENZENE ACTINOMADURA KIJANIATA SUGAR BIOSYNTHESIS KETOREDUCTASE TDP BINDING NADP BINDINGBINDING PROTEIN
Ref.: COMBINED STRUCTURAL AND FUNCTIONAL INVESTIGATION OF C-3''-KETOREDUCTASE INVOLVED IN THE BIOSYNTHESIS OF DTDP-L-DIGITOXOSE. BIOCHEMISTRY V. 50 5905 2011
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 3RCB - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 3RC7 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
3 3RBV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 3RC1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 3RC9 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 3RC2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 3RCB - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 3RC7 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
3 3RBV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 3RC1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 3RC9 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 3RC2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 families.
1 3RCB - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
2 3RC7 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
3 3RBV - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 3RC1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 3RC9 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 3RC2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAP; Similar ligands found: 127
No: Ligand ECFP6 Tc MDL keys Tc
1 NAP 1 1
2 NA0 0.881356 0.986301
3 TAP 0.872881 0.934211
4 NDO 0.840336 0.972603
5 NAD 0.811966 0.986111
6 N01 0.733871 0.958904
7 A3D 0.712 0.972603
8 NBP 0.707692 0.935065
9 NAD IBO 0.688 0.921053
10 NHD 0.68254 0.958904
11 NJP 0.661417 0.972973
12 NAJ PYZ 0.659091 0.898734
13 NFD 0.658915 0.934211
14 DND 0.619048 0.959459
15 NXX 0.619048 0.959459
16 ZID 0.605839 0.972603
17 NAQ 0.59854 0.922078
18 ATR 0.59292 0.917808
19 NAE 0.591241 0.946667
20 NDE 0.58042 0.986301
21 A22 0.571429 0.958904
22 AMP NAD 0.571429 0.933333
23 NAJ 0.567164 0.986111
24 A2R 0.563025 0.932432
25 NDC 0.561644 0.922078
26 NA7 0.552846 0.907895
27 ODP 0.551471 0.935065
28 A2P 0.539823 0.930556
29 8ID 0.537313 0.910256
30 NAD BBN 0.525974 0.865854
31 NPW 0.525547 0.8875
32 CNA 0.521739 0.959459
33 NZQ 0.521739 0.910256
34 NAD CJ3 0.519231 0.835294
35 NDP 0.514493 0.922078
36 PO4 PO4 A A A A PO4 0.503937 0.930556
37 DG1 0.503401 0.922078
38 1DG 0.503401 0.922078
39 NAD TDB 0.5 0.696078
40 TXP 0.5 0.922078
41 NMN AMP PO4 0.492958 0.921053
42 XNP 0.492958 0.875
43 25L 0.492308 0.958904
44 25A 0.492063 0.972222
45 NAD NDT 0.490909 0.747368
46 NMN 0.486726 0.888889
47 NGD 0.485714 0.935065
48 2AM 0.477876 0.891892
49 ADP 0.458333 0.945205
50 PAP 0.451613 0.931507
51 ADP MG 0.45082 0.906667
52 BEF ADP 0.447154 0.883117
53 ADP BEF 0.447154 0.883117
54 A2D 0.445378 0.945205
55 AN2 0.442623 0.932432
56 ADP PO3 0.44 0.944444
57 SAP 0.44 0.896104
58 AGS 0.44 0.896104
59 M33 0.439024 0.906667
60 AR6 AR6 0.438849 0.945205
61 BA3 0.438017 0.945205
62 ATP MG 0.436508 0.906667
63 ADP BMA 0.43609 0.92
64 OAD 0.43609 0.92
65 ATP 0.435484 0.945205
66 OOB 0.435115 0.958904
67 B4P 0.434426 0.945205
68 AP5 0.434426 0.945205
69 GAP 0.433071 0.92
70 0WD 0.432432 0.922078
71 5FA 0.432 0.945205
72 2A5 0.432 0.87013
73 AQP 0.432 0.945205
74 00A 0.428571 0.909091
75 CA0 0.427419 0.92
76 ALF ADP 0.426357 0.871795
77 ADP ALF 0.426357 0.871795
78 ACP 0.424 0.92
79 NAJ PZO 0.423841 0.897436
80 9SN 0.423358 0.897436
81 VO4 ADP 0.423077 0.932432
82 ANP MG 0.423077 0.896104
83 ADP VO4 0.423077 0.932432
84 WAQ 0.422222 0.884615
85 ACQ 0.421875 0.92
86 V3L 0.421875 0.945205
87 ADQ 0.421053 0.92
88 AR6 0.420635 0.918919
89 APR 0.420635 0.918919
90 ATP A A A 0.42029 0.958333
91 CO7 0.419753 0.786517
92 1ZZ 0.419118 0.841463
93 3OD 0.419118 0.92
94 DLL 0.41791 0.958904
95 AD9 0.417323 0.92
96 NAX 0.416667 0.875
97 OVE 0.416667 0.857143
98 MYR AMP 0.416058 0.841463
99 AV2 0.415385 0.868421
100 A3P 0.414634 0.944444
101 NNR 0.414414 0.72973
102 ALF ADP 3PG 0.413793 0.8625
103 OMR 0.413793 0.831325
104 LA8 ALF 3PG 0.413793 0.8625
105 ANP 0.410853 0.92
106 A1R 0.410448 0.860759
107 ABM 0.409836 0.893333
108 AMP 0.408333 0.944444
109 A 0.408333 0.944444
110 SON 0.408 0.933333
111 PPS 0.407692 0.829268
112 5AL 0.407692 0.932432
113 TYR AMP 0.407143 0.933333
114 NAI 0.406897 0.909091
115 7D3 0.406504 0.857143
116 DAL AMP 0.406015 0.932432
117 ADX 0.404762 0.829268
118 ATF 0.40458 0.907895
119 3UK 0.404412 0.945946
120 AMP DBH 0.404255 0.894737
121 139 0.402685 0.875
122 AMP MG 0.401639 0.893333
123 50T 0.401575 0.906667
124 SRP 0.401515 0.907895
125 A A 0.40146 0.972222
126 FA5 0.4 0.933333
127 3AM 0.4 0.90411
Ligand no: 2; Ligand: TLO; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 TLO 1 1
2 TPE 0.725275 0.946667
3 TTP 0.722892 0.945205
4 TYD 0.716049 0.945205
5 TMP 0.654321 0.931507
6 T3F 0.628866 0.909091
7 T3Q 0.628866 0.909091
8 18T 0.625 0.933333
9 TRH 0.625 0.933333
10 3R2 0.625 0.921053
11 TDX 0.625 0.945946
12 1JB 0.625 0.933333
13 DAU 0.618557 0.933333
14 DWN 0.612245 0.909091
15 3YN 0.612245 0.933333
16 T46 0.606061 0.933333
17 0N2 0.606061 0.897436
18 0FX 0.6 0.909091
19 MMF 0.6 0.909091
20 QDM 0.588235 0.897436
21 AKM 0.582524 0.864198
22 1YF 0.582524 0.921053
23 FNF 0.582524 0.921053
24 JHZ 0.582524 0.886076
25 4TG 0.576923 0.921053
26 FUH 0.554545 0.909091
27 QUH 0.554545 0.909091
28 TBD 0.549451 0.907895
29 T5A 0.521739 0.865854
30 THM 0.518519 0.849315
31 LLT 0.518519 0.849315
32 ATY 0.510417 0.894737
33 DT DT PST 0.509434 0.883117
34 0DN 0.506024 0.810811
35 DT DT DT DT DT 0.495238 0.92
36 UFP 0.494382 0.857143
37 UPP 0.49 0.878378
38 AZD 0.484848 0.860759
39 FDM 0.483516 0.87013
40 T3S 0.483516 0.792208
41 5IU 0.483516 0.857143
42 TXS 0.477778 0.769231
43 T3P 0.477273 0.891892
44 BRU 0.472527 0.857143
45 5HU 0.472527 0.918919
46 NYM 0.467391 0.906667
47 TQP 0.465116 0.888889
48 7SG 0.465116 0.888889
49 THP 0.462366 0.917808
50 T5K 0.461538 0.878049
51 T4K 0.461538 0.878049
52 DUT 0.453608 0.90411
53 ATM 0.453608 0.848101
54 D3T 0.453608 0.918919
55 DUD 0.442105 0.90411
56 BVP 0.438776 0.893333
57 4TA 0.435484 0.831325
58 DT ME6 DT 0.433333 0.871795
59 DT DT DT 0.431373 0.88
60 ABT 0.416667 0.839506
61 DCP 0.415842 0.844156
62 2DT 0.413043 0.905405
63 YYY 0.40404 0.844156
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3RC1; Ligand: TLO; Similar sites found: 75
This union binding pocket(no: 1) in the query (biounit: 3rc1.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1HDG NAD 0.006549 0.40407 1.80723
2 2FZW NAD 0.003033 0.4073 2
3 3BAZ NAP 0.00248 0.42139 2.1021
4 4J4H NAI 0.00116 0.42582 2.3166
5 4J4H 1J1 0.00116 0.42582 2.3166
6 4JK3 NAD 0.0006963 0.40121 2.3166
7 4DPL NAP 0.001828 0.4155 2.57143
8 5JE8 NAD 0.002692 0.41993 2.64901
9 2BH9 NAP 0.000158 0.50646 2.85714
10 5JCM ISD 0.00499 0.41392 2.88248
11 5JCM FAD 0.004802 0.41392 2.88248
12 5JCM NAD 0.005105 0.41353 2.88248
13 1CER NAD 0.005834 0.40351 3.02115
14 1ZMD NAI 0.004335 0.41144 3.14286
15 2NXE SAM 0.004807 0.42814 3.14961
16 4YCA NDP 0.001486 0.42747 3.40136
17 1Z82 NDP 0.005508 0.40197 3.58209
18 3ABI NAD 0.0006718 0.43218 3.71429
19 1D1T NAD 0.001453 0.40406 3.71429
20 4OOE NDP 0.01396 0.40138 3.71429
21 4OOE FOM 0.01396 0.40138 3.71429
22 2YYY NAP 0.0006465 0.40771 3.79009
23 1H9A NAP 0.001201 0.41213 3.91753
24 1YJQ NAP 0.001931 0.40194 3.9604
25 1M2W NAD 0.008559 0.40459 4
26 2JHF NAD 0.03319 0.40336 4
27 1CF2 NAP 0.0002319 0.41557 4.1543
28 1J0X NAD 0.003563 0.40469 4.21687
29 1GR0 NAD 0.001035 0.41446 4.28571
30 1QMG APX 0.01023 0.40129 4.28571
31 1MO9 FAD 0.01576 0.4008 4.28571
32 1BW9 NAD 0.002681 0.42928 4.49438
33 1C1X NAD 0.00405 0.40991 4.50704
34 5UAV NDP 0.0003664 0.43332 4.65839
35 5UAV TFB 0.0003664 0.43332 4.65839
36 1DLJ UGA 0.004838 0.40496 5.14286
37 1DLJ NAI 0.005467 0.40294 5.14286
38 1F06 NDP 0.001316 0.40277 5.625
39 5M67 3D1 0.004599 0.40497 6
40 5M67 NAD 0.004743 0.40446 6
41 3OND ADN 0.005545 0.40104 6
42 3OND NAD 0.005545 0.40104 6
43 2F1K NAP 0.0002243 0.41713 6.09319
44 3GGO ENO 0.001369 0.41814 6.36943
45 3GGO NAI 0.001369 0.41814 6.36943
46 3NJ4 NAD 0.01944 0.40935 6.57143
47 3NJ4 AFX 0.01944 0.40935 6.57143
48 2DT5 NAD 0.0001605 0.42809 6.63507
49 2NU8 COA 0.003779 0.40179 7.71429
50 2ZJ1 ARJ 0.003287 0.41219 8.28571
51 2ZJ1 NAD 0.003411 0.41158 8.28571
52 3OA2 NAD 0.000002405 0.53044 9.43396
53 2PV7 NAD 0.0003273 0.4127 9.73154
54 1U3U BNF 0.004028 0.40174 10
55 1U3U NAD 0.004028 0.40174 10
56 4KQW NAP 0.001133 0.41304 10.2857
57 1E5Q NDP 0.0004623 0.41362 11.1429
58 1NVM NAD 0.001534 0.40093 11.5385
59 2IXB NAD 0.00001911 0.48761 14.2857
60 2IXB A2G 0.00001316 0.46336 14.2857
61 1WP4 NDP 0.0002179 0.41918 15.2249
62 2CVZ NDP 0.0002723 0.41171 15.2249
63 3O9Z AKG 0.0000004325 0.48435 16.3462
64 3O9Z NAD 0.0000007727 0.4708 16.3462
65 3WBF API 0.0002128 0.43621 17.0492
66 3WBF NAP 0.0002136 0.42283 17.0492
67 4L8V NAP 0.0001113 0.43783 31.7507
68 4KOA NDP 0.000006135 0.43272 41.4414
69 2GLX NDP 0.0000001405 0.50981 42.1687
70 1RYD NDP 0.0000001395 0.55922 42.8571
71 1H6C NDP 0.0000001756 0.55558 42.8571
72 1H6C SIN 0.0000003265 0.54909 42.8571
73 5A04 NDP 0.0000001457 0.58333 43.0678
74 5A04 BGC 0.0000002054 0.58333 43.0678
75 1ZH8 NAP 0.0000005788 0.50471 45.8824
Pocket No.: 2; Query (leader) PDB : 3RC1; Ligand: NAP; Similar sites found: 57
This union binding pocket(no: 2) in the query (biounit: 3rc1.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1HDG NAD 0.005887 0.40931 1.80723
2 2FZW NAD 0.003119 0.40047 2
3 3BAZ NAP 0.002588 0.42413 2.1021
4 4J4H NAI 0.001055 0.42025 2.3166
5 4J4H 1J1 0.001055 0.42025 2.3166
6 4DPL NAP 0.001944 0.41804 2.57143
7 5JE8 NAD 0.002922 0.42195 2.64901
8 2BH9 NAP 0.0001813 0.50765 2.85714
9 5JCM NAD 0.00759 0.40097 2.88248
10 5JCM ISD 0.007713 0.40071 2.88248
11 5JCM FAD 0.007419 0.40071 2.88248
12 1CER NAD 0.005455 0.40804 3.02115
13 1ZMD NAI 0.004693 0.4134 3.14286
14 2NXE SAM 0.00587 0.42748 3.14961
15 4YCA NDP 0.001627 0.42949 3.40136
16 1Z82 NDP 0.002177 0.4215 3.58209
17 3ABI NAD 0.0005516 0.43928 3.71429
18 1H9A NAP 0.0009883 0.40369 3.91753
19 1M2W NAD 0.008656 0.40764 4
20 1CF2 NAP 0.0002755 0.40187 4.1543
21 1QMG APX 0.009163 0.40657 4.28571
22 1GR0 NAD 0.0009794 0.40454 4.28571
23 1BW9 NAD 0.001528 0.44346 4.49438
24 1C1X NAD 0.002322 0.42319 4.50704
25 5UAV NDP 0.0004883 0.41971 4.65839
26 5UAV TFB 0.0004883 0.41971 4.65839
27 4TO8 FLC 0.04188 0.40224 5.47945
28 2F1K NAP 0.0002314 0.40412 6.09319
29 3GGO ENO 0.001766 0.40728 6.36943
30 3GGO NAI 0.001766 0.40728 6.36943
31 3NJ4 NAD 0.01972 0.404 6.57143
32 3NJ4 AFX 0.02062 0.40321 6.57143
33 2DT5 NAD 0.00007135 0.42743 6.63507
34 3GFB NAD 0.006382 0.40274 6.85714
35 3JV7 NAD 0.003897 0.40631 7.82609
36 2ZJ1 ARJ 0.003046 0.40707 8.28571
37 2ZJ1 NAD 0.003099 0.4068 8.28571
38 3OA2 NAD 0.0000004762 0.56311 9.43396
39 2PV7 NAD 0.0003452 0.40068 9.73154
40 4KQW NAP 0.001218 0.40144 10.2857
41 1E5Q NDP 0.0004991 0.40074 11.1429
42 2IXB NAD 0.000003082 0.52238 14.2857
43 2IXB A2G 0.000003404 0.49261 14.2857
44 1WP4 NDP 0.0002301 0.40671 15.2249
45 3O9Z NAD 0.0000002618 0.49462 16.3462
46 3O9Z AKG 0.0000004683 0.49299 16.3462
47 3WBF API 0.0002034 0.42468 17.0492
48 3WBF NAP 0.0001484 0.41688 17.0492
49 4L8V NAP 0.00003223 0.44203 31.7507
50 4KOA NDP 0.000007731 0.41696 41.4414
51 2GLX NDP 0.00000002066 0.51851 42.1687
52 1RYD NDP 0.00000002864 0.5699 42.8571
53 1H6C NDP 0.00000004277 0.56383 42.8571
54 1H6C SIN 0.00000008135 0.55761 42.8571
55 5A04 BGC 0.00000005033 0.59321 43.0678
56 5A04 NDP 0.00000003527 0.59285 43.0678
57 1ZH8 NAP 0.00000007615 0.5149 45.8824
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