Receptor
PDB id Resolution Class Description Source Keywords
1UMK 1.75 Å EC: 1.6.2.2 THE STRUCTURE OF HUMAN ERYTHROCYTE NADH-CYTOCHROME B5 REDUCTASE HOMO SAPIENS FLAVOPROTEIN BETA BARREL FAD-BINDING DOMAIN NADH-BINDING DOMAIN OXIDOREDUCTASE
Ref.: STRUCTURE OF HUMAN ERYTHROCYTE NADH-CYTOCHROME B5 REDUCTASE. ACTA CRYSTALLOGR.,SECT.D V. 60 1929 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FAD A:1301;
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
3W2E 2.1 Å EC: 1.6.2.2 CRYSTAL STRUCTURE OF OXIDATION INTERMEDIATE (20 MIN) OF NADH CYTOCHROME B5 REDUCTASE FROM PIG LIVER SUS SCROFA REDUCTASE CYTOCHROME B5 OXIDOREDUCTASE
Ref.: ELUCIDATIONS OF THE CATALYTIC CYCLE OF NADH-CYTOCHR REDUCTASE BY X-RAY CRYSTALLOGRAPHY: NEW INSIGHTS IN REGULATION OF EFFICIENT ELECTRON TRANSFER J.MOL.BIOL. V. 425 4295 2013
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3W5H - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5GV8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 3W2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3W2I - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 5GV7 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 1UMK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 3W2H - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1NDH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 3W2G - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 3W2E - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3W5H - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 5GV8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 3W2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
4 3W2I - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 5GV7 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
6 1UMK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 3W2H - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
8 1NDH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 3W2G - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 3W2E - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
11 1QX4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
12 1IB0 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
13 1I7P - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CND - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
2 3W5H - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
3 5GV8 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 3W2F - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 3W2I - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 5GV7 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
7 1UMK - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 3W2H - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 1NDH - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 3W2G - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
11 3W2E - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
12 2EIX - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 1QX4 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
14 1IB0 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
15 1I7P - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FAD; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 6FA 0.794118 0.987654
6 DAL FAD PER 0.772414 0.951807
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 62F 0.572327 0.939024
12 F2N 0.566265 0.886364
13 FMN 0.543307 0.876543
14 FA9 0.526316 0.939759
15 6YU 0.516304 0.860215
16 CNV FAD 0.511905 0.908046
17 P6G FDA 0.511628 0.908046
18 FAD NBT 0.508876 0.83871
19 A2D 0.504065 0.875
20 P5F 0.491329 0.941176
21 FAD CNX 0.488506 0.8125
22 APR 0.488372 0.851852
23 AR6 0.488372 0.851852
24 AGS 0.484615 0.811765
25 SAP 0.484615 0.811765
26 M33 0.484375 0.864198
27 BA3 0.484127 0.875
28 FAD NBA 0.480663 0.802083
29 ATP 0.48062 0.851852
30 B4P 0.480315 0.875
31 ADP 0.480315 0.851852
32 AP5 0.480315 0.875
33 ANP 0.477273 0.831325
34 AQP 0.476923 0.851852
35 5FA 0.476923 0.851852
36 48N 0.469388 0.902439
37 OAD 0.467626 0.876543
38 GTA 0.465753 0.892857
39 AN2 0.465116 0.841463
40 AD9 0.462121 0.831325
41 3OD 0.460993 0.876543
42 RBF 0.460938 0.790123
43 FB0 0.460606 0.835165
44 139 0.460526 0.858824
45 AP0 0.46 0.835294
46 A22 0.459854 0.864198
47 ACP 0.458015 0.853659
48 8QN 0.456522 0.864198
49 PRX 0.454545 0.831325
50 A1R 0.453237 0.86747
51 G3A 0.452055 0.902439
52 T5A 0.45098 0.872093
53 G5P 0.44898 0.902439
54 ATF 0.448529 0.821429
55 50T 0.44697 0.819277
56 ACQ 0.444444 0.853659
57 PAJ 0.442857 0.847059
58 ADQ 0.442857 0.853659
59 5AL 0.441176 0.864198
60 ADX 0.439394 0.775281
61 CA0 0.439394 0.853659
62 A4P 0.437909 0.831461
63 25L 0.4375 0.864198
64 P33 FDA 0.436464 0.817204
65 5SV 0.435714 0.793103
66 TXE 0.434211 0.890244
67 OMR 0.434211 0.818182
68 ABM 0.434109 0.829268
69 A 0.433071 0.82716
70 AMP 0.433071 0.82716
71 4AD 0.432624 0.855422
72 ADJ 0.432258 0.818182
73 BIS 0.430556 0.802326
74 SRA 0.429688 0.788235
75 AFH 0.42953 0.825581
76 TXD 0.427632 0.890244
77 NXX 0.427632 0.865854
78 UP5 0.427632 0.878049
79 DND 0.427632 0.865854
80 6V0 0.427632 0.857143
81 SRP 0.42446 0.843373
82 PR8 0.423611 0.837209
83 TAT 0.423358 0.821429
84 AMO 0.422535 0.865854
85 PTJ 0.42069 0.835294
86 FYA 0.42069 0.864198
87 TXA 0.42069 0.865854
88 CNA 0.420382 0.865854
89 00A 0.41958 0.823529
90 AHX 0.41958 0.835294
91 MAP 0.41844 0.811765
92 NAI 0.418301 0.845238
93 AU1 0.41791 0.831325
94 AP2 0.416667 0.843373
95 A12 0.416667 0.843373
96 25A 0.415493 0.851852
97 AMP MG 0.415385 0.785714
98 COD 0.415094 0.842697
99 ADP BEF 0.414815 0.77907
100 BEF ADP 0.414815 0.77907
101 4TC 0.412903 0.879518
102 APC 0.411765 0.843373
103 NB8 0.410959 0.835294
104 ME8 0.410959 0.806818
105 1ZZ 0.410959 0.806818
106 4UW 0.409091 0.825581
107 NAX 0.409091 0.837209
108 RBY 0.408759 0.843373
109 ADV 0.408759 0.843373
110 ADP MG 0.407407 0.797619
111 P1H 0.405882 0.818182
112 OOB 0.405594 0.864198
113 A A 0.40411 0.829268
114 LAD 0.40411 0.825581
115 UPA 0.403846 0.86747
116 4UU 0.401316 0.833333
117 A3D 0.401235 0.876543
118 DLL 0.4 0.864198
119 XAH 0.4 0.806818
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3W2E; Ligand: NAD; Similar sites found: 92
This union binding pocket(no: 1) in the query (biounit: 3w2e.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RGE 2GP 0.03007 0.42383 None
2 3W9F I3P 0.03116 0.43999 1.53846
3 1FLM FMN 0.01667 0.40925 1.63934
4 2OG2 MLI 0.02313 0.43497 1.84502
5 3B9Q MLI 0.03519 0.42283 1.84502
6 1C9H RAP 0.04939 0.40877 1.86916
7 2YRX AMP 0.02677 0.42458 2.21402
8 4NRT 2NG 0.02126 0.43224 2.58303
9 1U6R IOM 0.03394 0.41402 2.58303
10 3W6X HZP 0.01047 0.44715 2.62009
11 2D3Y DU 0.01951 0.44092 2.73973
12 1NE7 16G 0.002426 0.48081 2.95203
13 5JSQ 6MS 0.04374 0.40102 3.24074
14 4F07 FAD 0.001929 0.44942 3.68421
15 5GXU FAD 0.00001615 0.51109 3.69004
16 2GJP MAL 0.02082 0.42393 3.69004
17 1KZL CRM 0.002099 0.47346 3.84615
18 1VHZ APR 0.0394 0.41765 4.0404
19 3L6C MLI 0.01912 0.43352 4.05904
20 2H7C SIA 0.02029 0.43189 4.05904
21 5A0U CHT 0.04149 0.40917 4.05904
22 3R5W F42 0.02212 0.40643 4.46429
23 1FLJ GSH 0.03055 0.42146 4.61538
24 3A3B FMN 0.0031 0.46964 4.73684
25 3A3B RBF 0.003635 0.46595 4.73684
26 1GOJ ADP 0.03982 0.4163 4.79705
27 4DFU QUE 0.03714 0.41179 4.79705
28 4LH7 1X8 0.01522 0.43945 5.16605
29 3GD4 NAD 0.01421 0.40125 5.47945
30 1DKU AP2 0.008164 0.42532 5.53506
31 1T5C ADP 0.0375 0.41514 5.53506
32 4K6B GLU 0.01286 0.44114 5.59006
33 2QX0 APC 0.03085 0.40889 5.66038
34 3BMN AX3 0.01993 0.43703 5.90406
35 3F5A SIA GAL NAG 0.01935 0.45071 6.09756
36 1WK9 TSB 0.02302 0.41543 6.16438
37 3BY9 SIN 0.0487 0.41178 6.53846
38 1PVC ILE SER GLU VAL 0.007338 0.46337 6.64207
39 4QVB F42 0.01431 0.4065 6.80272
40 2WBV SIA 0.04389 0.40037 6.87831
41 5E5U 1PS 0.003137 0.4959 7.03518
42 4WOE 3S5 0.03451 0.41501 7.38007
43 4L6H HCS 0.04714 0.41107 7.38007
44 4H2D FMN 0.02533 0.40067 8.48485
45 4RHS SIA SIA GAL 0.02917 0.42001 8.48709
46 3DGY 2GP 0.04319 0.41446 9.27835
47 5O0X FAD 0.00000589 0.60624 10.3321
48 2QTZ FAD 0.0000006 0.62453 10.7011
49 2QTZ NAP 0.00001544 0.48549 10.7011
50 2W5P CL8 0.03889 0.41871 12.7517
51 4YHB FAD 0.0005958 0.45412 14.2857
52 5VW2 FDA 0.000000008839 0.57308 16.2362
53 5VW2 NAP 0.000000008839 0.57308 16.2362
54 5H5J FAD 0.0000004549 0.42951 16.2362
55 1TLL FAD 0.000001074 0.59871 16.6052
56 1F20 FAD 0.000001354 0.59408 16.6052
57 1F20 NAP 0.001823 0.467 16.6052
58 1TLL NAP 0.0008332 0.44801 16.6052
59 4DQL FAD 0.000006737 0.54057 17.3432
60 4DQL NAP 0.00000414 0.49561 17.3432
61 1DDG FAD 0.00002463 0.53105 18.0812
62 3FJO FAD 0.000001497 0.60558 18.8192
63 3QFS NAP 0.0000213 0.47086 18.8192
64 3QFS FAD 0.0000213 0.47086 18.8192
65 3CRZ FAD 0.000001468 0.58617 19.8444
66 3CRZ NAP 0.00000005943 0.56861 19.8444
67 1A8P FAD 0.000006009 0.5644 20.155
68 2VNI FAD 0.000002196 0.50878 20.2952
69 2VNI A2P 0.000002196 0.50878 20.2952
70 1QFY FAD 0.000000007426 0.5661 20.4545
71 1QFY NAP 0.000000007426 0.5661 20.4545
72 3MHP FAD 0.0000004934 0.42932 21.2838
73 2PIA FMN 0.00002777 0.53391 22.8782
74 2BSA FAD 0.000000003465 0.54153 23.2472
75 2BSA NAP 0.000000003773 0.53567 23.2472
76 3VO1 FAD 0.0000002642 0.64953 24.3542
77 1EWY FAD 0.0000003604 0.65127 25.0923
78 3JQQ A2P 0.0000002075 0.51206 26.1993
79 3JQQ FAD 0.0002873 0.42388 26.1993
80 1GAW FAD 0.00000005844 0.69058 27.6753
81 3OZV FAD 0.00006974 0.43541 27.6753
82 1FND A2P 0.00000006445 0.57669 28.4133
83 1FND FAD 0.00000006445 0.57669 28.4133
84 1KRH FAD 0.000001537 0.59155 29.1513
85 1SM4 FAD 0.0000001268 0.66506 29.5203
86 2RC5 FAD 0.0000008869 0.60251 32.1033
87 4U9U FAD 0.0000005909 0.60396 32.8413
88 4YRY NAD 0.000000124 0.51047 32.8413
89 2XNJ NAP 0.00005339 0.52089 36.0902
90 2XNJ FAD 0.00008753 0.48512 36.0902
91 4WQM FAD 0.0000004803 0.5954 38.0074
92 4G1V FAD 0.000001 0.46017 39.8524
Pocket No.: 2; Query (leader) PDB : 3W2E; Ligand: FAD; Similar sites found: 92
This union binding pocket(no: 2) in the query (biounit: 3w2e.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RGE 2GP 0.03007 0.42383 None
2 3W9F I3P 0.03116 0.43999 1.53846
3 1FLM FMN 0.01667 0.40925 1.63934
4 2OG2 MLI 0.02313 0.43497 1.84502
5 3B9Q MLI 0.03519 0.42283 1.84502
6 1C9H RAP 0.04939 0.40877 1.86916
7 2YRX AMP 0.02677 0.42458 2.21402
8 4NRT 2NG 0.02126 0.43224 2.58303
9 1U6R IOM 0.03394 0.41402 2.58303
10 3W6X HZP 0.01047 0.44715 2.62009
11 2D3Y DU 0.01951 0.44092 2.73973
12 1NE7 16G 0.002426 0.48081 2.95203
13 5JSQ 6MS 0.04374 0.40102 3.24074
14 4F07 FAD 0.001929 0.44942 3.68421
15 5GXU FAD 0.00001615 0.51109 3.69004
16 2GJP MAL 0.02082 0.42393 3.69004
17 1KZL CRM 0.002099 0.47346 3.84615
18 1VHZ APR 0.0394 0.41765 4.0404
19 3L6C MLI 0.01912 0.43352 4.05904
20 2H7C SIA 0.02029 0.43189 4.05904
21 5A0U CHT 0.04149 0.40917 4.05904
22 3R5W F42 0.02212 0.40643 4.46429
23 1FLJ GSH 0.03055 0.42146 4.61538
24 3A3B FMN 0.0031 0.46964 4.73684
25 3A3B RBF 0.003635 0.46595 4.73684
26 1GOJ ADP 0.03982 0.4163 4.79705
27 4DFU QUE 0.03714 0.41179 4.79705
28 4LH7 1X8 0.01522 0.43945 5.16605
29 3GD4 NAD 0.01421 0.40125 5.47945
30 1DKU AP2 0.008164 0.42532 5.53506
31 1T5C ADP 0.0375 0.41514 5.53506
32 4K6B GLU 0.01286 0.44114 5.59006
33 2QX0 APC 0.03085 0.40889 5.66038
34 3BMN AX3 0.01993 0.43703 5.90406
35 3F5A SIA GAL NAG 0.01935 0.45071 6.09756
36 1WK9 TSB 0.02302 0.41543 6.16438
37 3BY9 SIN 0.0487 0.41178 6.53846
38 1PVC ILE SER GLU VAL 0.007338 0.46337 6.64207
39 4QVB F42 0.01431 0.4065 6.80272
40 2WBV SIA 0.04389 0.40037 6.87831
41 5E5U 1PS 0.003137 0.4959 7.03518
42 4WOE 3S5 0.03451 0.41501 7.38007
43 4L6H HCS 0.04714 0.41107 7.38007
44 4H2D FMN 0.02533 0.40067 8.48485
45 4RHS SIA SIA GAL 0.02917 0.42001 8.48709
46 3DGY 2GP 0.04319 0.41446 9.27835
47 5O0X FAD 0.00000589 0.60624 10.3321
48 2QTZ FAD 0.0000006 0.62453 10.7011
49 2QTZ NAP 0.00001544 0.48549 10.7011
50 2W5P CL8 0.03889 0.41871 12.7517
51 4YHB FAD 0.0005958 0.45412 14.2857
52 5VW2 FDA 0.000000008839 0.57308 16.2362
53 5VW2 NAP 0.000000008839 0.57308 16.2362
54 5H5J FAD 0.0000004549 0.42951 16.2362
55 1TLL FAD 0.000001074 0.59871 16.6052
56 1F20 FAD 0.000001354 0.59408 16.6052
57 1F20 NAP 0.001823 0.467 16.6052
58 1TLL NAP 0.0008332 0.44801 16.6052
59 4DQL FAD 0.000006737 0.54057 17.3432
60 4DQL NAP 0.00000414 0.49561 17.3432
61 1DDG FAD 0.00002463 0.53105 18.0812
62 3FJO FAD 0.000001497 0.60558 18.8192
63 3QFS NAP 0.0000213 0.47086 18.8192
64 3QFS FAD 0.0000213 0.47086 18.8192
65 3CRZ FAD 0.000001468 0.58617 19.8444
66 3CRZ NAP 0.00000005943 0.56861 19.8444
67 1A8P FAD 0.000006009 0.5644 20.155
68 2VNI FAD 0.000002196 0.50878 20.2952
69 2VNI A2P 0.000002196 0.50878 20.2952
70 1QFY FAD 0.000000007426 0.5661 20.4545
71 1QFY NAP 0.000000007426 0.5661 20.4545
72 3MHP FAD 0.0000004934 0.42932 21.2838
73 2PIA FMN 0.00002777 0.53391 22.8782
74 2BSA FAD 0.000000003465 0.54153 23.2472
75 2BSA NAP 0.000000003773 0.53567 23.2472
76 3VO1 FAD 0.0000002642 0.64953 24.3542
77 1EWY FAD 0.0000003604 0.65127 25.0923
78 3JQQ A2P 0.0000002075 0.51206 26.1993
79 3JQQ FAD 0.0002873 0.42388 26.1993
80 1GAW FAD 0.00000005844 0.69058 27.6753
81 3OZV FAD 0.00006974 0.43541 27.6753
82 1FND A2P 0.00000006445 0.57669 28.4133
83 1FND FAD 0.00000006445 0.57669 28.4133
84 1KRH FAD 0.000001537 0.59155 29.1513
85 1SM4 FAD 0.0000001268 0.66506 29.5203
86 2RC5 FAD 0.0000008869 0.60251 32.1033
87 4U9U FAD 0.0000005909 0.60396 32.8413
88 4YRY NAD 0.000000124 0.51047 32.8413
89 2XNJ NAP 0.00005339 0.52089 36.0902
90 2XNJ FAD 0.00008753 0.48512 36.0902
91 4WQM FAD 0.0000004803 0.5954 38.0074
92 4G1V FAD 0.000001 0.46017 39.8524
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