Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
84.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.73
Reason: strain 84.5 kcal/mol
strain ΔE 84.5 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
79% of hydrophobic surface is solvent-exposed (15/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.748 kcal/mol/HA)
✓ Good fit quality (FQ -7.29)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Extreme strain energy (84.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.188
kcal/mol
LE
-0.748
kcal/mol/HA
Fit Quality
-7.29
FQ (Leeson)
HAC
31
heavy atoms
MW
464
Da
LogP
3.62
cLogP
Interaction summary
HB 14
HY 2
PI 1
CLASH 3
⚠ Exposure 78%
Interaction summary
HB 14
HY 2
PI 1
CLASH 3
⚠ Exposure 78%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
79% of hydrophobic surface is solvent-exposed (15/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 19
Buried (contacted) 4
Exposed 15
LogP 3.62
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.369 | Score | -23.188 |
|---|---|---|---|
| Inter norm | -1.016 | Intra norm | 0.268 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 14 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 84.5 | ||
| Residues |
ALA158
ALA24
ASN126
ASP129
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 10 | Strict recall | 0.67 |
| HB same residue+role | 8 | HB role recall | 0.73 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 120 | 1.614569869255919 | -0.669416 | -15.982 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 99 | 4.091520828763953 | -1.00638 | -23.5555 | 13 | 21 | 16 | 0.76 | 0.64 | - | no | Open |
| 531 | 4.369056809288307 | -1.01642 | -23.1883 | 14 | 21 | 16 | 0.76 | 0.73 | - | no | Current |
| 61 | 4.977878823863977 | -1.01627 | -24.7884 | 14 | 21 | 16 | 0.76 | 0.73 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.188kcal/mol
Ligand efficiency (LE)
-0.7480kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.287
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
464.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.62
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
84.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.50kcal/mol
Minimised FF energy
-16.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
705.8Ų
Total solvent-accessible surface area of free ligand
BSA total
577.8Ų
Buried surface area upon binding
BSA apolar
370.8Ų
Hydrophobic contacts buried
BSA polar
207.0Ų
Polar contacts buried
Fraction buried
81.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1337.3Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
505.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)