Molecular metrics status: missing
Molecular metrics have not been computed yet for this pose.
No cached metrics
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
Metrics pending
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA pending
Strain ΔE
41.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.90, Jaccard 0.83, H-bond role recall 0.27
Reason: no major geometry red flags detected
2 protein-contact clashes
55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Interaction summary
HB 5
HY 7
PI 2
CLASH 2
⚠ Exposure 54%
Interaction summary
HB 5
HY 7
PI 2
CLASH 2
⚠ Exposure 54%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 10
Exposed 12
LogP 4.12
H-bonds 5
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.479 | Score | -27.162 |
|---|---|---|---|
| Inter norm | -1.087 | Intra norm | 0.211 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 5 |
| Artifact reason | excluded; hard geometry fail; 1 severe clash; 3 protein clashes; high strain Δ 41.6 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLU21
GLU73
GLY23
GLY25
LEU130
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
THR44
THR69
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 19 | Native recall | 0.90 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 550 | 4.479461706606301 | -1.08685 | -27.1623 | 5 | 21 | 19 | 0.90 | 0.27 | - | yes | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.