Receptor
PDB id Resolution Class Description Source Keywords
4RVU 1.8 Å EC: 1.-.-.- THE NATIVE STRUCTURE OF MYCOBACTERIAL RV1454C COMPLEXED WITH MYCOBACTERIUM TUBERCULOSIS QOR QUINONE ELECTRON TRANSFER MYCOBACTERIUM TUBERCULOSISCATALYZE TRANSFER OF ELECTRONS FROM NADPH TO SUBSTRATES ELTRANSPORT
Ref.: STRUCTURAL VIEWS OF QUINONE OXIDOREDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS REVEAL LARGE CONFORMATIO CHANGES INDUCED BY THE CO-FACTOR. FEBS J. V. 282 2697 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP D:401;
A:401;
C:401;
B:401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RVU 1.8 Å EC: 1.-.-.- THE NATIVE STRUCTURE OF MYCOBACTERIAL RV1454C COMPLEXED WITH MYCOBACTERIUM TUBERCULOSIS QOR QUINONE ELECTRON TRANSFER MYCOBACTERIUM TUBERCULOSISCATALYZE TRANSFER OF ELECTRONS FROM NADPH TO SUBSTRATES ELTRANSPORT
Ref.: STRUCTURAL VIEWS OF QUINONE OXIDOREDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS REVEAL LARGE CONFORMATIO CHANGES INDUCED BY THE CO-FACTOR. FEBS J. V. 282 2697 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 4RVU - 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 247 families.
1 4RVU - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
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 3JYN - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 4RVU - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 3QWB - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
4 1QOR - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 159
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 DG1 0.68 1
8 1DG 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 2AM 0.529412 0.87013
23 6V0 0.519685 0.974026
24 NAP 0.514493 0.922078
25 EAD 0.507143 0.949367
26 A2D 0.504673 0.921053
27 TXE 0.503876 0.935897
28 NA0 0.496454 0.910256
29 TXD 0.496124 0.911392
30 SAP 0.495575 0.875
31 AGS 0.495575 0.875
32 P1H 0.493056 0.925926
33 CO7 0.489796 0.791209
34 TAP 0.489362 0.864198
35 PAP 0.482456 0.907895
36 BA3 0.481818 0.921053
37 NAJ PZO 0.478261 0.924051
38 ATP 0.477876 0.921053
39 B4P 0.477477 0.921053
40 ADP 0.477477 0.921053
41 AP5 0.477477 0.921053
42 OAD 0.47541 0.897436
43 5FA 0.473684 0.921053
44 AR6 0.473684 0.896104
45 APR 0.473684 0.896104
46 AQP 0.473684 0.921053
47 AN2 0.473214 0.909091
48 3OD 0.467742 0.897436
49 50T 0.464912 0.884615
50 PO4 PO4 A A A A PO4 0.463415 0.857143
51 V3L 0.461538 0.896104
52 2A5 0.46087 0.85
53 A1R 0.459016 0.841463
54 ADQ 0.459016 0.897436
55 4AD 0.459016 0.875
56 OVE 0.458716 0.8375
57 OMR 0.458647 0.813953
58 PPS 0.457627 0.811765
59 AD9 0.456897 0.897436
60 CA0 0.45614 0.897436
61 M33 0.45614 0.884615
62 ADJ 0.455882 0.879518
63 A3P 0.455357 0.894737
64 ACP 0.452174 0.897436
65 ENP 0.451613 0.85
66 UP5 0.451128 0.948052
67 SRP 0.45 0.8625
68 ANP 0.449153 0.897436
69 ACQ 0.449153 0.897436
70 PRX 0.448276 0.82716
71 5AL 0.445378 0.884615
72 7D4 0.443478 0.8375
73 ADX 0.443478 0.811765
74 AMP 0.436364 0.894737
75 A 0.436364 0.894737
76 4TC 0.433824 0.924051
77 7D3 0.433628 0.8375
78 ETB 0.433566 0.797753
79 DCA 0.433566 0.788889
80 1ZZ 0.433071 0.802326
81 BIS 0.433071 0.864198
82 00A 0.432 0.864198
83 ATF 0.429752 0.886076
84 0T1 0.427586 0.788889
85 5SV 0.427419 0.788235
86 8QN 0.427419 0.884615
87 3AM 0.427273 0.857143
88 N01 0.426573 0.884615
89 PR8 0.425197 0.811765
90 WAQ 0.425197 0.841463
91 LAD 0.425197 0.821429
92 DTP 0.425 0.8375
93 AMO 0.424 0.886076
94 PAJ 0.424 0.843373
95 APC 0.423729 0.886076
96 UPA 0.423358 0.935897
97 48N 0.422222 0.853659
98 FYA 0.421875 0.860759
99 PTJ 0.421875 0.853659
100 CNA 0.421429 0.910256
101 PUA 0.42069 0.9125
102 NXX 0.419118 0.910256
103 DND 0.419118 0.910256
104 AV2 0.418033 0.848101
105 COA 0.417808 0.788889
106 3UK 0.417323 0.897436
107 OOB 0.416 0.909091
108 IVC 0.415584 0.78022
109 DAT 0.415254 0.8375
110 NDO 0.414966 0.897436
111 139 0.414286 0.901235
112 3AT 0.413223 0.896104
113 TAT 0.413223 0.886076
114 YLB 0.413043 0.784091
115 62F 0.4125 0.823529
116 ABM 0.412281 0.848101
117 YAP 0.412214 0.875
118 YLP 0.411765 0.784091
119 ME8 0.410853 0.802326
120 NB8 0.410853 0.853659
121 SON 0.410256 0.886076
122 DLL 0.409449 0.909091
123 AHX 0.409449 0.853659
124 COS 0.409396 0.771739
125 AMX 0.409396 0.797753
126 CAO 0.409396 0.763441
127 30N 0.409396 0.72449
128 7D5 0.409091 0.8125
129 4UW 0.408759 0.9125
130 APX 0.407692 0.841463
131 SRA 0.40708 0.85
132 CMX 0.406667 0.788889
133 SCO 0.406667 0.788889
134 TYM 0.405797 0.886076
135 COD 0.405594 0.777778
136 OXK 0.405229 0.771739
137 CA6 0.405229 0.70297
138 A12 0.405172 0.886076
139 AP2 0.405172 0.886076
140 9SN 0.40458 0.853659
141 LAQ 0.404412 0.802326
142 T5A 0.404255 0.914634
143 FAM 0.403974 0.771739
144 ACO 0.403974 0.763441
145 FCX 0.403974 0.763441
146 AMP MG 0.403509 0.825
147 VO4 ADP 0.403226 0.860759
148 ADP VO4 0.403226 0.860759
149 YLC 0.402878 0.823529
150 1VU 0.402597 0.763441
151 FA5 0.401515 0.886076
152 HAX 0.401316 0.771739
153 APU 0.4 0.923077
154 TXA 0.4 0.886076
155 A U 0.4 0.898734
156 4UU 0.4 0.948052
157 AFH 0.4 0.843373
158 CAJ 0.4 0.771739
159 AR6 AR6 0.4 0.871795
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RVU; Ligand: NDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4rvu.bio2) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RVU; Ligand: NDP; Similar sites found: 114
This union binding pocket(no: 2) in the query (biounit: 4rvu.bio2) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5C2N NAG 0.01974 0.42745 None
2 2CVQ NDP 0.002406 0.41354 1.22324
3 3KB6 NAD 0.0008769 0.43362 1.50602
4 3NJ4 AFX 0.00484 0.435 1.80723
5 3NJ4 NAD 0.00484 0.435 1.80723
6 2J5V RGP 0.02447 0.42249 1.80723
7 1X7D ORN 0.001448 0.41283 1.80723
8 1X7D NAD 0.001103 0.40395 1.80723
9 3ABI NAD 0.000518 0.41446 2.10843
10 5MDH NAD 0.003228 0.41118 2.10843
11 2GZ3 NAP 0.005873 0.40093 2.10843
12 4YMJ 4EJ 0.04111 0.40701 2.30263
13 1SC6 NAD 0.00125 0.40621 2.40964
14 1KYQ NAD 0.02269 0.40002 2.55474
15 4JK3 NAD 0.0003032 0.41357 2.7027
16 2GCG NDP 0.0008797 0.40428 2.72727
17 5GZ6 NDP 0.003614 0.4269 2.76074
18 5GZ6 7C3 0.005424 0.41304 2.76074
19 3OND ADN 0.0009854 0.42944 3.01205
20 3OND NAD 0.0009854 0.42944 3.01205
21 2VHW NAI 0.001229 0.41424 3.01205
22 1OMO NAD 0.002231 0.4263 3.10559
23 5HVJ ANP 0.022 0.42228 3.49206
24 5DH3 5BS 0.006542 0.41867 3.49206
25 1E5Q NDP 0.001051 0.42757 3.61446
26 3V1Y NAD 0.002136 0.42113 3.61446
27 5LD5 NAD 0.002857 0.42489 3.91566
28 4XYB NDP 0.001704 0.40666 3.91566
29 2CDC XYP 0.008444 0.40489 3.91566
30 2CDC NAP 0.01009 0.40184 3.91566
31 2CDC XYS 0.01009 0.40184 3.91566
32 1J49 NAD 0.00215 0.41545 4.21687
33 5CAE COA 0.008367 0.4023 4.21687
34 1F06 2NP 0.002145 0.40306 4.375
35 1F06 NDP 0.002145 0.40306 4.375
36 4RDH AMP 0.006499 0.42925 4.51389
37 3BMN AX3 0.01089 0.42814 4.51389
38 2NAD NAD 0.001027 0.41584 4.51807
39 1V8B NAD 0.0004284 0.43086 4.81928
40 5FCF GLY GLY GLY 0.02068 0.4077 4.81928
41 1TE2 PGA 0.04278 0.41042 4.86726
42 1P77 ATR 0.01426 0.43261 5.14706
43 1NYT NAP 0.003254 0.41655 5.16605
44 1Q1Y BB2 0.02946 0.4008 5.2356
45 1U8X NAD 0.001821 0.42391 5.42169
46 1P31 EPU 0.0171 0.40275 5.42169
47 2YLN CYS 0.02131 0.42591 5.65371
48 2DT5 NAD 0.0003889 0.44439 5.6872
49 1LSS NAD 0.005925 0.41741 5.71429
50 2D2I NAP 0.0019 0.43242 5.72289
51 3B20 NAD 0.005235 0.41083 5.72289
52 5M67 NAD 0.0008634 0.43254 6.3253
53 5M67 ADE 0.0009335 0.43126 6.3253
54 5M67 3D1 0.001181 0.42738 6.3253
55 2VYN NAD 0.00218 0.41521 6.62651
56 1SBR VIB 0.02189 0.42251 7.5
57 5DN9 NAD 0.00136 0.40776 7.83133
58 3NGL NAP 0.003516 0.42743 8.33333
59 3AB4 THR 0.0417 0.40342 8.42697
60 1U1I NAD 0.0014 0.40973 8.43373
61 4J4H NAI 0.0007569 0.43281 8.88031
62 4J4H 1J1 0.0007569 0.43281 8.88031
63 4JCA CIT 0.005199 0.42996 8.98204
64 5BXV MGP 0.02468 0.42912 9.09091
65 1P0F NAP 0.00002886 0.46482 9.63855
66 1D1T NAD 0.00008026 0.46078 9.63855
67 1DMH MCT 0.0367 0.40638 9.6463
68 4RQU NAD 0.0002017 0.42751 9.93976
69 4BVA T3 0.001627 0.41212 9.93976
70 4BVA NDP 0.0007553 0.41203 9.93976
71 4CJX NAP 0.006248 0.40491 10.0313
72 4LH7 1X8 0.03507 0.414 10.5263
73 1U3U BNF 0.0001045 0.42289 11.4458
74 1U3U NAD 0.0001045 0.42289 11.4458
75 1NVM NAD 0.000504 0.41733 11.747
76 2HK9 ATR 0.006331 0.44208 12
77 2HK9 NAP 0.00376 0.41121 12
78 1CDO NAD 0.00008044 0.47852 12.6506
79 1E3I CXF 0.0003511 0.4241 12.6506
80 2FZW NAD 0.0007122 0.43078 12.9518
81 1QXA GLY GLY GLY 0.0339 0.40147 13.617
82 1CER NAD 0.001795 0.42417 13.8973
83 2ZB3 NDP 0.00006321 0.4861 15.9639
84 3TWO NDP 0.0000009314 0.52579 16.2651
85 2ZB4 NAP 0.000000007962 0.57638 16.5663
86 2ZB4 5OP 0.00000000899 0.56785 16.5663
87 1YKF NAP 0.0007377 0.43062 17.4699
88 5H81 NAP 0.0001438 0.48428 17.9949
89 1YQD NAP 0.000004505 0.49674 18.306
90 1KEV NDP 0.000445 0.42765 19.8795
91 2JHF NAD 0.0009882 0.4691 25.3012
92 5VKT NAP 0.000003057 0.49239 27.0718
93 1N9G NAP 0.0000008201 0.5641 27.1084
94 4WAS NAP 0.000007229 0.4952 27.1084
95 4WAS COO 0.00001041 0.48945 27.1084
96 5FI3 NAP 0.00006391 0.47134 28.3133
97 2DM6 NAP 0.00000000252 0.62476 30.1205
98 2DM6 IMN 0.0000000158 0.59742 30.1205
99 4W6Z 8ID 0.0005235 0.45999 31.3253
100 5DP2 NAP 0.00000004428 0.54274 31.5789
101 3WLE NAD 0.00001562 0.48306 31.9648
102 2DFV NAD 0.0001414 0.42731 34.3373
103 3GFB NAD 0.0003391 0.44997 34.6386
104 1H2B NAJ 0.005823 0.41437 35.241
105 3JV7 NAD 0.000003751 0.4891 37.9518
106 4GKV NAD 0.000004166 0.50063 38.3929
107 1LLU NAD 0.00001032 0.48646 40.0602
108 5DOZ NDP 0.0000004381 0.54022 40.9639
109 4IDC NDP 0.0000008552 0.52177 41.8675
110 4IDC 1XX 0.0000008552 0.52177 41.8675
111 4A0S NAP 0.00000003191 0.59233 43.0723
112 1PL6 572 0.001546 0.40368 43.0723
113 1R37 NAD 0.006461 0.41373 43.9759
114 4JBI NDP 0.000005575 0.4641 44.2771
115 1YB5 NAP 0.0000009243 0.52415 50
Pocket No.: 3; Query (leader) PDB : 4RVU; Ligand: NDP; Similar sites found: 13
This union binding pocket(no: 3) in the query (biounit: 4rvu.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1J6X MET 0.04047 0.40971 None
2 4RJD TFP 0.04389 0.40528 None
3 2I3G NAP 0.003263 0.40341 2.27273
4 5JE8 NAD 0.009624 0.40242 2.98013
5 1PU7 39A 0.04359 0.40576 3.21101
6 2XKO AKG 0.0145 0.43409 3.6036
7 1MUU NAD 0.008049 0.40038 3.91566
8 2WGH DTP 0.03502 0.40033 3.91566
9 1C1X NAD 0.0006715 0.40003 3.91566
10 2NNJ 225 0.04159 0.40348 4.51807
11 4RLQ 3SK 0.04281 0.40662 5.12048
12 2O4C NAD 0.001581 0.40007 6.92771
13 2DBZ NAP 0.0009036 0.4038 13.7725
Pocket No.: 4; Query (leader) PDB : 4RVU; Ligand: NDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4rvu.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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