Receptor
PDB id Resolution Class Description Source Keywords
2CWH 1.7 Å EC: 1.5.1.- CRYSTAL STRUCTURE OF DELTA1-PIPERIDEINE-2-CARBOXYLATE REDUCTASE FROM PSEUDOMONAS SYRINGAE COMPLEXED WITH NADPH A ND PYRROLE-2-CARBOXYLATE PSEUDOMONAS SYRINGAE PV. TOMATO NADPH DEPENDENT ENZYME OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF DELTA1-PIPERIDEINE-2-CARBOXYLATE/DELTA1-PYRROLINE-2-CARBOXYLATE REDUCTASE BELONGING TO A NEW FAMILY OF NAD(P)H-DEPENDENT OXIDOREDUCTASES: CONFORMATIONAL CHANGE, SUBSTRATE RECOGNITION, AND STEREOCHEMISTRY OF THE REACTION J.BIOL.C
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:2510;
B:1510;
Valid;
Valid;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
PYC A:2520;
B:1520;
Valid;
Valid;
none;
none;
submit data
110.091 C5 H4 N O2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CWH 1.7 Å EC: 1.5.1.- CRYSTAL STRUCTURE OF DELTA1-PIPERIDEINE-2-CARBOXYLATE REDUCTASE FROM PSEUDOMONAS SYRINGAE COMPLEXED WITH NADPH A ND PYRROLE-2-CARBOXYLATE PSEUDOMONAS SYRINGAE PV. TOMATO NADPH DEPENDENT ENZYME OXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURES OF DELTA1-PIPERIDEINE-2-CARBOXYLATE/DELTA1-PYRROLINE-2-CARBOXYLATE REDUCTASE BELONGING TO A NEW FAMILY OF NAD(P)H-DEPENDENT OXIDOREDUCTASES: CONFORMATIONAL CHANGE, SUBSTRATE RECOGNITION, AND STEREOCHEMISTRY OF THE REACTION J.BIOL.C
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CWH - PYC C5 H4 N O2 c1cc([nH]c....
2 2CWF - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CWH - PYC C5 H4 N O2 c1cc([nH]c....
2 2CWF - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2CWH - PYC C5 H4 N O2 c1cc([nH]c....
2 2CWF - NDP C21 H30 N7 O17 P3 c1nc(c2c(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
Ligand no: 2; Ligand: PYC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 PYC 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CWH; Ligand: NDP; Similar sites found: 84
This union binding pocket(no: 1) in the query (biounit: 2cwh.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CQK PIO 0.03281 0.40959 None
2 4NZ6 DGL 0.007092 0.44498 1.91693
3 3SHR CMP 0.021 0.40954 2.00669
4 1Q19 SSC 0.005142 0.45567 2.04082
5 1GOJ ADP 0.04619 0.41041 2.04082
6 2QS8 MET 0.0333 0.40306 2.04082
7 2VVG ADP 0.04342 0.41232 2.33236
8 3H4L ANP 0.009653 0.40815 2.33236
9 4GO7 THR 0.01257 0.42084 2.5
10 2CXG GLC GLC 0.004369 0.46026 2.62391
11 1GPM AMP 0.004523 0.45315 2.62391
12 3L8G GMB 0.02144 0.41726 2.6738
13 2G30 ALA ALA PHE 0.01703 0.4184 2.71318
14 3BY8 MLT 0.03466 0.40481 2.8169
15 3TY5 ATP 0.01382 0.41875 2.91545
16 3TDV GDP 0.01568 0.40174 2.94118
17 5FUI APY 0.0226 0.41701 3.0303
18 4FK7 P34 0.02269 0.41486 3.05677
19 5JBX MLI 0.03574 0.40537 3.06513
20 3BJE URA 0.041 0.40411 3.207
21 3N9R TD3 0.02405 0.40656 3.25733
22 2WZ5 MET 0.01275 0.40452 3.26797
23 4U00 ADP 0.02205 0.41816 3.27869
24 1O9W NAG 0.03884 0.40662 3.38983
25 3UEC ALA ARG TPO LYS 0.0239 0.41643 3.42466
26 3S6X SIA GAL BGC 0.02323 0.41535 3.69231
27 5LFV SIA GAL NAG 0.006271 0.46007 3.78549
28 2WDQ TEO 0.00815 0.4396 3.79009
29 5FJJ MAN 0.02016 0.43591 3.79009
30 3LRE ADP 0.04472 0.41139 3.79009
31 5FPE 3TR 0.04446 0.40616 3.79009
32 2G50 ALA 0.03177 0.40039 3.79009
33 5GVR LMR 0.0132 0.43784 3.84615
34 3SJK LYS PRO VAL LEU ARG THR ALA 0.03768 0.40593 4.21053
35 1WLJ U5P 0.03143 0.40303 4.2328
36 5AOG IAC 0.04862 0.40574 4.23453
37 1KSK URA 0.03592 0.40371 4.2735
38 3AB4 THR 0.004748 0.44693 4.49438
39 3WG3 A2G GAL NAG FUC 0.01219 0.42576 4.49438
40 2DTJ THR 0.01042 0.42495 4.49438
41 3N2O AG2 0.03694 0.40665 4.66472
42 4FOU C2E 0.02634 0.40094 4.92424
43 2X1L MET 0.0354 0.40545 4.95627
44 1G6H ADP 0.03147 0.40873 5.05837
45 5L3S G 0.03351 0.40561 5.06757
46 1PNF NDG NAG 0.01313 0.42544 5.09554
47 1U0J ADP 0.01539 0.42051 5.24345
48 1RL4 BRR 0.01727 0.42226 5.24781
49 3BP1 GUN 0.0215 0.40227 5.51724
50 4Y4V DAL 0.01625 0.43782 5.60472
51 3RC3 ANP 0.02133 0.41315 5.8309
52 3A4M ADP 0.01717 0.4224 6.15385
53 4CCK OGA 0.02632 0.41404 6.41399
54 1VBO MAN MAN MAN 0.04394 0.40269 6.41399
55 5E5U MLI 0.005997 0.46157 6.53266
56 1XPJ TLA 0.003098 0.46894 7.14286
57 1RZM E4P 0.04122 0.40162 7.39645
58 2IDO TMP 0.01786 0.42357 7.52688
59 5H9P TD2 0.0256 0.41315 7.59494
60 3FW3 GLC 0.01096 0.44515 7.89474
61 5AHO TLA 0.03723 0.40162 9.52381
62 2H88 TEO 0.02465 0.40988 10.7143
63 1GXU 2HP 0.01361 0.43945 10.989
64 3PNA CMP 0.03678 0.4008 11.039
65 2J5V PCA 0.0295 0.41684 11.0787
66 3LN9 FLC 0.004818 0.43089 11.5108
67 3NOJ PYR 0.02807 0.41831 12.605
68 2GN2 C5P 0.04929 0.40693 13.1579
69 5URY PAM 0.03121 0.42423 14.3836
70 4WVW SLT 0.02603 0.40727 15.2778
71 4YMU ATP 0.03412 0.40251 16.8182
72 4NFD SIA 0.01876 0.42193 19.1667
73 2BOS GLA GAL GLC NBU 0.005955 0.44364 22.0588
74 2BOS GLA GAL 0.007632 0.42211 22.0588
75 2BOS GLA GAL GLC 0.009222 0.41638 22.0588
76 2DT9 THR 0.006345 0.44043 26.3473
77 4CCN OGA 0.03962 0.40433 28.5714
78 1Z2I NAD 0.0000000001832 0.68532 38.1924
79 1S20 NAD 0.000002392 0.57039 42.3529
80 2X06 NAD 0.00000001153 0.64276 42.8571
81 4FJU NAI 0.000000007195 0.60789 44.3149
82 4FJU GLV 0.00000002004 0.58225 44.3149
83 1VBI NAD 0.000000004775 0.61372 45.7726
84 1V9N NDP 0.000000001341 0.65255 47.2303
Pocket No.: 2; Query (leader) PDB : 2CWH; Ligand: NDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2cwh.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2CWH; Ligand: PYC; Similar sites found: 85
This union binding pocket(no: 3) in the query (biounit: 2cwh.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CQK PIO 0.03953 0.40959 None
2 2Z9I GLY ALA THR VAL 0.02127 0.42749 1.85185
3 4NZ6 DGL 0.008743 0.44498 1.91693
4 3SHR CMP 0.02473 0.41056 2.00669
5 1Q19 SSC 0.00633 0.45567 2.04082
6 3AVS OGA 0.01521 0.42555 2.04082
7 2QS8 MET 0.02561 0.41774 2.04082
8 2VVG ADP 0.04992 0.41334 2.33236
9 3H4L ANP 0.01437 0.40513 2.33236
10 4GO7 THR 0.01561 0.42084 2.5
11 4XDA RIB 0.02547 0.4099 2.589
12 1GPM AMP 0.005509 0.45315 2.62391
13 2CXG GLC GLC 0.01125 0.4443 2.62391
14 3L8G GMB 0.02614 0.41726 2.6738
15 2G30 ALA ALA PHE 0.02002 0.4184 2.71318
16 4FK7 P34 0.02706 0.41486 3.05677
17 3BJE URA 0.04897 0.40411 3.207
18 2UYQ SAM 0.04899 0.40749 3.22581
19 4U00 ADP 0.02646 0.41816 3.27869
20 1O9W NAG 0.04816 0.4058 3.38983
21 3UEC ALA ARG TPO LYS 0.02863 0.41643 3.42466
22 4XDY HIO 0.03679 0.41216 3.5503
23 4X1Z FUC GAL NDG 0.03685 0.41612 3.61446
24 2YIP YIO 0.02888 0.40269 3.62319
25 3S6X SIA GAL BGC 0.02785 0.41535 3.69231
26 2ZL7 FUC GAL NGA 0.03606 0.4078 3.72881
27 5TV6 PML 0.02954 0.41035 3.75
28 4D3S BOG 0.02172 0.41741 3.75427
29 5LFV SIA GAL NAG 0.008302 0.45835 3.78549
30 2WDQ TEO 0.01008 0.4396 3.79009
31 5FJJ MAN 0.02348 0.43591 3.79009
32 3LRE ADP 0.04513 0.41571 3.79009
33 2G50 ALA 0.03648 0.40182 3.79009
34 5GVR LMR 0.01567 0.43784 3.84615
35 5KIQ SIA GAL NAG FUC 0.03004 0.41585 4.06091
36 3SJK LYS PRO VAL LEU ARG THR ALA 0.04507 0.40593 4.21053
37 1KSK URA 0.04254 0.40371 4.2735
38 4K6B GLU 0.01518 0.43002 4.34783
39 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.03206 0.41316 4.37318
40 3AB4 THR 0.005953 0.44693 4.49438
41 3WG3 A2G GAL NAG FUC 0.01375 0.42787 4.49438
42 2DTJ THR 0.01298 0.42495 4.49438
43 2X1L MET 0.04238 0.40545 4.95627
44 1G6H ADP 0.03755 0.40873 5.05837
45 5L3S G 0.04016 0.40561 5.06757
46 1PNF NDG NAG 0.01678 0.42514 5.09554
47 1U0J ADP 0.01896 0.42051 5.24345
48 1RL4 BRR 0.02803 0.41561 5.24781
49 4L4J NAG NAG BMA MAN NAG 0.0102 0.42546 5.42986
50 3BP1 GUN 0.008711 0.4439 5.51724
51 4Y4V DAL 0.01946 0.43782 5.60472
52 3RC3 ANP 0.02614 0.41315 5.8309
53 4FGC PQ0 0.04928 0.4027 6.06061
54 3A4M ADP 0.02217 0.42114 6.15385
55 5E5U MLI 0.007134 0.46157 6.53266
56 1MFI FHC 0.03022 0.41285 7.01754
57 1XPJ TLA 0.00374 0.46894 7.14286
58 5H9P TD2 0.03112 0.41315 7.59494
59 3FW3 GLC 0.01294 0.44515 7.89474
60 4CUB GAL NAG 0.01433 0.43474 8.19672
61 4WBD CIT 0.03207 0.41213 9.32945
62 5AHO TLA 0.04407 0.40162 9.52381
63 2H88 TEO 0.03014 0.40988 10.7143
64 1GXU 2HP 0.01614 0.43945 10.989
65 3PNA CMP 0.03224 0.40833 11.039
66 2J5V PCA 0.03485 0.41684 11.0787
67 2P4T NAP 0.03046 0.40588 11.2903
68 3LN9 FLC 0.005787 0.43089 11.5108
69 3ZVS MLI 0.04636 0.40953 11.875
70 1QKQ MAN 0.01143 0.41796 11.9718
71 3NOJ PYR 0.03318 0.41831 12.605
72 5URY PAM 0.03704 0.42423 14.3836
73 4YMU ATP 0.04148 0.40251 16.8182
74 4NFD SIA 0.02147 0.42214 19.1667
75 2BOS GLA GAL GLC NBU 0.007272 0.44364 22.0588
76 2BOS GLA GAL 0.007409 0.42524 22.0588
77 2BOS GLA GAL GLC 0.009218 0.41903 22.0588
78 2DT9 THR 0.007922 0.44043 26.3473
79 1Z2I NAD 0.000000001701 0.65764 38.1924
80 1S20 NAD 0.000003668 0.56943 42.3529
81 2X06 NAD 0.00000001949 0.64229 42.8571
82 4FJU GLV 0.000000007745 0.61337 44.3149
83 4FJU NAI 0.00000001622 0.60702 44.3149
84 1VBI NAD 0.00000004239 0.5911 45.7726
85 1V9N NDP 0.000000005849 0.60064 47.2303
Pocket No.: 4; Query (leader) PDB : 2CWH; Ligand: PYC; 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: 2cwh.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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