Receptor
PDB id Resolution Class Description Source Keywords
3RI3 2.29 Å EC: 1.3.1.- ACTINORHODIN POLYKETIDE KETOREDUCTASE MUTANT P94L BOUND TO N THE INHIBITOR EMODIN STREPTOMYCES COELICOLOR ACTINORHODIN POLYKETIDE KETOREDUCTASE SHORT-CHAIN DEHYDROGENASE/REDUCTASE ROSSMANN FOLD TYPE II POLYKETIDE KETOREDUCTASE OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMP
Ref.: STRUCTURAL AND BIOCHEMICAL ANALYSES OF REGIO- AND STEREOSPECIFICITIES OBSERVED IN A TYPE II POLYKETID KETOREDUCTASE. BIOCHEMISTRY V. 50 4638 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EMO A:302;
A:303;
B:302;
B:303;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
270.237 C15 H10 O5 Cc1cc...
NDP A:301;
B:301;
 Valid;
Valid;
 none;
none;
 submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RH4 2.3 Å EC: 1.3.1.- ACTINORHODIN KETOREDUCTASE, ACTKR, WITH NADPH AND INHIBITOR STREPTOMYCES COELICOLOR OXIDOREDUCTASE POLYKETIDE ACTINORHODIN KETOREDUCTASE COMBINATORIAL BIOSYNTHESIS SHORT CHAIN DEHYDROGENASE/REDUC
Ref.: INHIBITION KINETICS AND EMODIN COCRYSTAL STRUCTURE II POLYKETIDE KETOREDUCTASE BIOCHEMISTRY V. 47 1837 2008
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1X7H - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 1X7G - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 2RH4 Ki = 15 uM EMO C15 H10 O5 Cc1cc2c(c(....
4 1W4Z - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 2RHR - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
6 3RI3 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
7 2RHC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3SJU - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 1X7H - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 1X7G - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 2RH4 Ki = 15 uM EMO C15 H10 O5 Cc1cc2c(c(....
5 1W4Z - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
6 2RHR - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
7 3RI3 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
8 2RHC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (89)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1E6W - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1E3S - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 3A28 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3SJU - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
5 1X7H - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
6 1W4Z - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
7 2RHR - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
8 3RI3 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
9 2RHC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 1Q7B Kd = 3.5 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
11 1Q7C - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
12 1GEG - GLC C6 H12 O6 C([C@@H]1[....
13 4N5N - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
14 4QEC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
15 4QED - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
16 3AY6 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
17 3AUU - BGC C6 H12 O6 C([C@@H]1[....
18 3AUT - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
19 4BO0 ic50 = 0.2 uM FXE C17 H18 N4 O3 Cn1c2cccc(....
20 4AG3 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
21 4BO2 ic50 = 0.05 uM 36K C17 H18 N4 O2 CCn1c2cccc....
22 4BNX ic50 = 0.02 uM O74 C20 H14 Cl N3 O c1ccc2c(c1....
23 4BNU ic50 = 0.02 uM 9KQ C16 H11 N5 c1ccc(cc1)....
24 4BO3 ic50 = 0.3 uM U98 C12 H10 F3 N3 O2 S c1cc(cc(c1....
25 4BNZ ic50 = 0.26 uM 8M5 C16 H14 N2 O Cn1cc(c2c1....
26 4NBT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
27 1IPF - TNE C8 H13 N O CN1[C@H]2C....
28 5OVK - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
29 1NFQ - AOI n/a n/a
30 6CI9 - F3V C3 H7 N O CC(=O)CN
31 2ZTU - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
32 2ZTM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
33 1X1T - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
34 5O72 Ki = 23 nM 9MH C18 H14 F N3 O3 c1cc(cc2c1....
35 5HS6 - J3Z C18 H22 O2 C[C@]12CC[....
36 5L7W Ki = 11 nM 6QU C18 H11 F2 N O4 c1cc(c(c(c....
37 5O6O Ki = 58 nM 9MB C17 H11 F2 N O3 c1cc(c(c(c....
38 5ICM - GLC C6 H12 O6 C([C@@H]1[....
39 5O7C Ki = 9 nM 9N2 C17 H9 F N2 O2 c1cc(cc2c1....
40 5JS6 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
41 5JSF - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
42 4JP3 - CIT C6 H8 O7 C(C(=O)O)C....
43 4NBW - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
44 2Q2Q - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
45 1DOH Ki = 2.4 nM NID C9 H5 N O3 c1cc2c(c(c....
46 4ITU - 1HS C5 H12 O4 S2 C[C@@H](CS....
47 4RF2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
48 1GCO - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
49 1G6K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50 1GEE - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
51 5EPO - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
52 4URE - 1PS C8 H11 N O3 S c1cc[n+](c....
53 4URF - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
54 4NBU - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
55 4KWI - 1TJ C19 H12 O5 Cc1cc2c(c(....
56 4OSO - 2V4 C19 H14 O6 C[C@]1(Cc2....
57 5OJG - BUO C4 H6 O2 CC(=O)C(=O....
58 5OJI - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
59 4FN4 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
60 5WUW - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
61 2EWM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
62 2B4Q - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
63 6F9Q - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
64 3AI3 - SOL C6 H12 O6 C([C@@H]([....
65 3AI2 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
66 1IY8 Ki = 23.8 mM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
67 4CR7 - MAN C6 H12 O6 C([C@@H]1[....
68 5ITV - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
69 4ZA2 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70 1FMC - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
71 1AHH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
72 5B4V - DXX C4 H6 O4 CC(C(=O)O)....
73 5B4U - MLA C3 H4 O4 C(C(=O)O)C....
74 5FF9 ic50 = 5230 uM AEF C8 H11 N O c1cc(ccc1C....
75 5FFF ic50 = 425 uM 5XC C8 H6 O3 c1cc2c(cc1....
76 6JHA - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
77 6JHB - ENO C9 H8 O4 c1cc(ccc1C....
78 3U4C - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
79 5THQ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
80 1AE1 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
81 1PR9 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
82 1WNT - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
83 2BGM - NAJ C21 H27 N7 O14 P2 c1cc(c[n+]....
84 2GDZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
85 6IXM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
86 1HDC Ki = 1 uM CBO C34 H50 O7 CC1([C@@H]....
87 3QWI ic50 = 2.8 uM CUE C15 H8 O5 c1cc2c(cc1....
88 3AFN - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
89 6J7U - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: EMO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 EMO 1 1
Ligand no: 2; Ligand: NDP; Similar ligands found: 179
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 EAD 0.507143 0.949367
27 7L1 0.507143 0.763441
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 HQG 0.483051 0.909091
38 PAP 0.482456 0.907895
39 BA3 0.481818 0.921053
40 NAJ PZO 0.478261 0.924051
41 HEJ 0.477876 0.921053
42 ATP 0.477876 0.921053
43 AP5 0.477477 0.921053
44 B4P 0.477477 0.921053
45 ADP 0.477477 0.921053
46 OAD 0.47541 0.897436
47 5FA 0.473684 0.921053
48 AQP 0.473684 0.921053
49 APR 0.473684 0.896104
50 AR6 0.473684 0.896104
51 AN2 0.473214 0.909091
52 3OD 0.467742 0.897436
53 50T 0.464912 0.884615
54 NAJ PYZ 0.464789 0.879518
55 9X8 0.463415 0.851852
56 PO4 PO4 A A A A PO4 0.463415 0.857143
57 V3L 0.461538 0.896104
58 2A5 0.46087 0.85
59 AT4 0.460177 0.886076
60 4AD 0.459016 0.875
61 A1R 0.459016 0.841463
62 ADQ 0.459016 0.897436
63 OVE 0.458716 0.8375
64 OMR 0.458647 0.813953
65 PPS 0.457627 0.811765
66 AD9 0.456897 0.897436
67 M33 0.45614 0.884615
68 CA0 0.45614 0.897436
69 ADJ 0.455882 0.879518
70 A3P 0.455357 0.894737
71 ACP 0.452174 0.897436
72 KG4 0.452174 0.897436
73 ENP 0.451613 0.85
74 UP5 0.451128 0.948052
75 SRP 0.45 0.8625
76 ACQ 0.449153 0.897436
77 ANP 0.449153 0.897436
78 PRX 0.448276 0.82716
79 A3R 0.447154 0.841463
80 5AL 0.445378 0.884615
81 ADX 0.443478 0.811765
82 7D4 0.443478 0.8375
83 8LQ 0.442623 0.8625
84 8LH 0.438017 0.8625
85 6YZ 0.438017 0.897436
86 AMP 0.436364 0.894737
87 A 0.436364 0.894737
88 4TC 0.433824 0.924051
89 7D3 0.433628 0.8375
90 DCA 0.433566 0.788889
91 ETB 0.433566 0.797753
92 8LE 0.433333 0.851852
93 BIS 0.433071 0.864198
94 1ZZ 0.433071 0.802326
95 00A 0.432 0.864198
96 ATF 0.429752 0.886076
97 DQV 0.428571 0.934211
98 0T1 0.427586 0.788889
99 5SV 0.427419 0.788235
100 8QN 0.427419 0.884615
101 3AM 0.427273 0.857143
102 N01 0.426573 0.884615
103 WAQ 0.425197 0.841463
104 LAD 0.425197 0.821429
105 PR8 0.425197 0.811765
106 DTP 0.425 0.8375
107 AMO 0.424 0.886076
108 PAJ 0.424 0.843373
109 APC 0.423729 0.886076
110 UPA 0.423358 0.935897
111 48N 0.422222 0.853659
112 FYA 0.421875 0.860759
113 PTJ 0.421875 0.853659
114 CNA 0.421429 0.910256
115 PUA 0.42069 0.9125
116 NXX 0.419118 0.910256
117 DND 0.419118 0.910256
118 AV2 0.418033 0.848101
119 COA 0.417808 0.788889
120 3UK 0.417323 0.897436
121 OOB 0.416 0.909091
122 IVC 0.415584 0.78022
123 DAT 0.415254 0.8375
124 NDO 0.414966 0.897436
125 139 0.414286 0.901235
126 B5V 0.414062 0.886076
127 T99 0.413223 0.886076
128 TAT 0.413223 0.886076
129 3AT 0.413223 0.896104
130 YLB 0.413043 0.784091
131 62F 0.4125 0.823529
132 ABM 0.412281 0.848101
133 45A 0.412281 0.848101
134 B5M 0.412214 0.875
135 YAP 0.412214 0.875
136 YLP 0.411765 0.784091
137 ME8 0.410853 0.802326
138 NB8 0.410853 0.853659
139 SON 0.410256 0.886076
140 DLL 0.409449 0.909091
141 AHX 0.409449 0.853659
142 AMX 0.409396 0.797753
143 30N 0.409396 0.72449
144 CAO 0.409396 0.763441
145 COS 0.409396 0.771739
146 7D5 0.409091 0.8125
147 4UW 0.408759 0.9125
148 F2R 0.408451 0.825581
149 APX 0.407692 0.841463
150 SRA 0.40708 0.85
151 CMX 0.406667 0.788889
152 SCO 0.406667 0.788889
153 TYM 0.405797 0.886076
154 COD 0.405594 0.777778
155 OXK 0.405229 0.771739
156 CA6 0.405229 0.70297
157 A12 0.405172 0.886076
158 AP2 0.405172 0.886076
159 OZV 0.404762 0.896104
160 9SN 0.40458 0.853659
161 LAQ 0.404412 0.802326
162 T5A 0.404255 0.914634
163 FAM 0.403974 0.771739
164 FCX 0.403974 0.763441
165 ACO 0.403974 0.763441
166 VO4 ADP 0.403226 0.860759
167 ADP VO4 0.403226 0.860759
168 YLC 0.402878 0.823529
169 1VU 0.402597 0.763441
170 FA5 0.401515 0.886076
171 B5Y 0.401515 0.875
172 HAX 0.401316 0.771739
173 AR6 AR6 0.4 0.871795
174 APU 0.4 0.923077
175 TXA 0.4 0.886076
176 AFH 0.4 0.843373
177 A U 0.4 0.898734
178 4UU 0.4 0.948052
179 CAJ 0.4 0.771739
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RH4; Ligand: EMO; Similar sites found with APoc: 102
This union binding pocket(no: 1) in the query (biounit: 2rh4.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 4O0L NDP 32.3636
2 4O0L NDP 32.3636
3 4O0L NDP 32.3636
4 4O0L NDP 32.3636
5 5O98 NAP 33.574
6 3WXB NDP 36.2007
7 3WXB NDP 36.2007
8 3RKR NAP 38.9892
9 6OW4 NAD 39.7112
10 6OW4 NAD 39.7112
11 6OW4 NAD 39.7112
12 6OW4 NAD 39.7112
13 6OW4 NAD 39.7112
14 6OW4 NAD 39.7112
15 1E3W NAD 42.5287
16 1E3W NAD 42.5287
17 1E3W NAD 42.5287
18 1E3W NAD 42.5287
19 1E6W NAD 42.6923
20 1E6W NAD 42.6923
21 1E6W NAD 42.6923
22 1E6W NAD 42.6923
23 3QWI NAP 43.7037
24 3QWI NAP 43.7037
25 3AFN NAP 43.7985
26 3AFN NAP 43.7985
27 3AFN NAP 43.7985
28 3AFN NAP 43.7985
29 1XG5 NAP 44.0433
30 1XG5 NAP 44.0433
31 1XG5 NAP 44.0433
32 1XG5 NAP 44.0433
33 5OVL NAP 44.7653
34 5OVL NAP 44.7653
35 5OVL NAP 44.7653
36 5OVL NAP 44.7653
37 6CI9 NAP 44.7876
38 6CI9 NAP 44.7876
39 6CI9 NAP 44.7876
40 6CI9 NAP 44.7876
41 3U4C NDP 44.8399
42 5T2U NAP 45.1613
43 5T2U NAP 45.1613
44 5T2U NAP 45.1613
45 5T2U NAP 45.1613
46 5O42 9JW 45.2555
47 5O42 BGC 45.2555
48 5O42 NAD 45.2555
49 4QED NAP 45.5645
50 4QED NAP 45.5645
51 4QED NAP 45.5645
52 4QED NAP 45.5645
53 3OID NDP 45.7364
54 3OID NDP 45.7364
55 3OID NDP 45.7364
56 3OID NDP 45.7364
57 5EJ2 NAD 45.8484
58 5EJ2 NAD 45.8484
59 3A28 NAD 46.124
60 3A28 NAD 46.124
61 3A28 NAD 46.124
62 3A28 NAD 46.124
63 1AE1 NAP 46.5201
64 1AE1 NAP 46.5201
65 1GEG NAD 46.875
66 1GEG NAD 46.875
67 1GEG NAD 46.875
68 1GEG NAD 46.875
69 4RF2 NAP 47.0588
70 4RF2 NAP 47.0588
71 5ITV NAI 47.0588
72 5ITV NAI 47.0588
73 5ITV NAI 47.0588
74 5ITV NAI 47.0588
75 4ITU NAI 47.5836
76 4ITU NAI 47.5836
77 4ITU NAI 47.5836
78 4ITU NAI 47.5836
79 4ITU 1HS 47.5836
80 4ITU 1HS 47.5836
81 1NFQ NAI 48.0769
82 1NFQ NAI 48.0769
83 1NFQ NAI 48.0769
84 1NFQ NAI 48.0769
85 1PR9 NAP 48.3607
86 1PR9 NAP 48.3607
87 3D3W NAP 48.3607
88 3D3W NAP 48.3607
89 5THQ NDP 48.8971
90 5THQ NDP 48.8971
91 5THQ NDP 48.8971
92 5THQ NDP 48.8971
93 3O03 NAP 49.0975
94 1YXM ADE 49.0975
95 1IY8 NAD 49.4382
96 1IY8 NAD 49.4382
97 1IY8 NAD 49.4382
98 1IY8 NAD 49.4382
99 4NBW NAD 49.8054
100 4NBW NAD 49.8054
101 4NBW NAD 49.8054
102 4NBW NAD 49.8054
103 4FN4 NAD 50
104 4FN4 NAD 50
105 4FN4 NAD 50
106 4FN4 NAD 50
Pocket No.: 2; Query (leader) PDB : 2RH4; Ligand: EMO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2rh4.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
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