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Receptor
PDB id Resolution Class Description Source Keywords
4HA9 2.35 Å EC: 1.1.1.302 STRUCTURAL INSIGHTS INTO THE REDUCTION MECHANISM OF SACCHARO CEREVISIA RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7 SACCHAROMYCES CEREVISIAE REDUCTASE NADPH BINDING OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO SACCHAROMYC CEREVISIAE RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7. PLOS ONE V. 8 61249 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:301;
Valid;
none;
Ka = 15000 M^-1
745.421 C21 H30 N7 O17 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4HA9 2.35 Å EC: 1.1.1.302 STRUCTURAL INSIGHTS INTO THE REDUCTION MECHANISM OF SACCHARO CEREVISIA RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7 SACCHAROMYCES CEREVISIAE REDUCTASE NADPH BINDING OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO SACCHAROMYC CEREVISIAE RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7. PLOS ONE V. 8 61249 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4HA9 Ka = 15000 M^-1 NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4HA9 Ka = 15000 M^-1 NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4HA9 Ka = 15000 M^-1 NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
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 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
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 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4HA9; Ligand: NDP; Similar sites found with APoc: 150
This union binding pocket(no: 1) in the query (biounit: 4ha9.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3DFR NDP None
2 1FWV SGA MAG FUC None
3 1R6N 434 None
4 2WOR 2AN None
5 4WG0 CHD None
6 4PYA 2X3 1.24224
7 4G86 BNT 1.60643
8 5TQZ GLC 2
9 1YNS HPO 2.00803
10 5ZI9 FLC 2.00803
11 6GAS FAD 2.00803
12 2NW9 FT6 2.00803
13 2F5X ASP 2.00803
14 2VVG ADP 2.00803
15 3FIU POP 2.00803
16 4ZNO SUC 2.38806
17 3B8I OXL 2.40964
18 5NM7 GLY 2.40964
19 4YRY NAD 2.40964
20 4B5W PYR 2.40964
21 5HWK BEZ 2.40964
22 4YRY FAD 2.40964
23 5BXA MAN 2.40964
24 2FZH DH1 2.42718
25 3RG9 NDP 2.5
26 3RG9 WRA 2.5
27 3NOJ PYR 2.52101
28 3TW1 AHN 2.53165
29 5E5U MLI 2.81124
30 2BO4 FLC 2.81124
31 1PVS 7HP 2.81124
32 3BP1 GUN 2.81124
33 1MVN PCO 2.87081
34 1MVN FMN 2.87081
35 3B6C SDN 2.99145
36 1JUV NDP 3.10881
37 4LIK CIT 3.21285
38 4XFR CIT 3.21285
39 2IYF UDP 3.21285
40 6F5W KG1 3.21285
41 5C9P FUC 3.21285
42 5WPJ NDP 3.21285
43 5B0I BOG 3.21285
44 5GVR LMR 3.4188
45 5YRG BGC GLC 3.52113
46 4EIL NDP 3.61446
47 3KJS NAP 3.61446
48 3KJS DQ1 3.61446
49 4LHD GLY 3.61446
50 2AWN ADP 3.61446
51 3LAD FAD 3.61446
52 2XT3 ADP 3.61446
53 4JWK CTN 3.62694
54 4NTO 1PW 3.86473
55 1Q19 SSC 4.01606
56 4WBD CIT 4.01606
57 1ZPD CIT 4.01606
58 1KC7 PPR 4.01606
59 2IYA UDP 4.01606
60 3HGM ATP 4.08163
61 5YRI GLC GLC 4.22535
62 1U70 MTX 4.30108
63 1U70 NDP 4.30108
64 1U72 NDP 4.30108
65 1U72 MTX 4.30108
66 4G05 JZ3 4.41767
67 4U8P UDP 4.41767
68 3LRE ADP 4.41767
69 3EYK EYK 4.65116
70 3NRR NAP 4.81928
71 3NRR D16 4.81928
72 1MJH ATP 4.93827
73 2KIN ADP 5
74 4KM2 ATR 5.02793
75 4KM2 TOP 5.02793
76 4USI AKG 5.19481
77 5FJJ MAN 5.22088
78 2HJR CIT 5.22088
79 4A4Z ANP 5.22088
80 1MFI FHC 5.26316
81 3AJ4 SEP 5.35714
82 6EOA FMN 5.62249
83 5ZBL AMP 5.62249
84 2ACV UDP 5.62249
85 1T9D P22 5.62249
86 3W6X HZP 5.67686
87 3EEL 53T 5.72687
88 2HYQ MAN MAN 5.7377
89 2GUD MAN 5.7377
90 2HYR BGC GLC 5.7377
91 2GUC MAN 5.7377
92 2NUO BGC 5.7377
93 1DR1 NAP 5.82011
94 1DR1 HBI 5.82011
95 5AJU RP5 5.83942
96 2P3V SRT 5.85938
97 2BL9 NDP 5.88235
98 2BL9 CP6 5.88235
99 2VBF TPP 6.0241
100 4A9C B5F 6.4257
101 3IAE D7K 6.4257
102 3JUC PCA 6.53595
103 1F4F TP3 6.82731
104 3FPF TNA 7.04698
105 3FPF MTA 7.04698
106 3VY6 BGC BGC 7.0922
107 1Q8O MAN MMA 7.22892
108 6C90 ADP 7.22892
109 4OR7 NAP 7.27273
110 2W9S NDP 7.45342
111 3AB1 FAD 7.63052
112 1D1G NDP 7.7381
113 2BQP GLC 8.11966
114 4PU6 ASP 8.39695
115 4I7E PEP 8.43373
116 1NLM UD1 8.51648
117 2CIG 1DG 8.80503
118 4LAE NAP 8.98204
119 4LAE 1VM 8.98204
120 5A96 GTP 9.23695
121 3IX9 NDP 9.63855
122 3TDC 0EU 10.0402
123 1NXJ TLA 10.0402
124 1OYY AGS 10.0402
125 2I5F 5IP 10.0917
126 1OFS SUC 10.1604
127 6CB2 OLC 10.2389
128 1AOE GW3 10.4167
129 1AOE NDP 10.4167
130 5JCM NAD 10.4418
131 5JCM FAD 10.4418
132 5JCM ISD 10.4418
133 3KP6 SAL 10.596
134 1J3I NDP 10.8434
135 1J3I WRA 10.8434
136 4DP3 NDP 10.8434
137 4DP3 MMV 10.8434
138 6EV2 BGC 11.5207
139 2DRC MTX 11.9497
140 5DXV NAP 12.1795
141 4M7V NAP 12.5714
142 4M7V RAR 12.5714
143 2J5V PCA 13.253
144 5TWB FAD 14.4578
145 5LXT 7AK 15.261
146 3HCH RSM 15.7534
147 3IA4 NDP 23.4568
148 3KPE TM3 25.641
149 4XT8 NAP 26.506
150 4XT8 TMQ 26.506
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