Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
34.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.52, H-bond role recall 0.27
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (20/32 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.524 kcal/mol/HA)
✓ Good fit quality (FQ -5.37)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Very high strain energy (34.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-19.401
kcal/mol
LE
-0.524
kcal/mol/HA
Fit Quality
-5.37
FQ (Leeson)
HAC
37
heavy atoms
MW
504
Da
LogP
1.92
cLogP
Interaction summary
HB 7
HY 6
PI 0
CLASH 3
⚠ Exposure 62%
Interaction summary
HB 7
HY 6
PI 0
CLASH 3
⚠ Exposure 62%
Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (20/32 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 32
Buried (contacted) 12
Exposed 20
LogP 1.92
H-bonds 7
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.307 | Score | -19.401 |
|---|---|---|---|
| Inter norm | -0.825 | Intra norm | 0.300 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 7 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; high strain Δ 34.2 | ||
| Residues |
ALA158
ALA24
ALA70
ASN126
ASP68
GLN42
GLU73
GLY23
GLY25
GLY47
GLY71
LEU31
LEU39
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
THR45
THR69
| ||
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 | ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.52 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 137 | 3.3070041617009425 | -0.824506 | -19.4015 | 7 | 23 | 15 | 0.71 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.401kcal/mol
Ligand efficiency (LE)
-0.5244kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.368
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
503.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.92
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
250.51kcal/mol
Minimised FF energy
216.35kcal/mol
SASA & burial
✓ computed
SASA (unbound)
772.3Ų
Total solvent-accessible surface area of free ligand
BSA total
656.4Ų
Buried surface area upon binding
BSA apolar
610.5Ų
Hydrophobic contacts buried
BSA polar
45.9Ų
Polar contacts buried
Fraction buried
85.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1588.8Ų
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
506.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)