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
27.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.57, Jaccard 0.44, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
79% of hydrophobic surface is solvent-exposed (22/28 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 (-0.831 kcal/mol/HA)
✓ Good fit quality (FQ -8.39)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (22)
Score
-29.101
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-8.39
FQ (Leeson)
HAC
35
heavy atoms
MW
463
Da
LogP
4.98
cLogP
Interaction summary
HB 12
HY 2
PI 0
CLASH 5
⚠ Exposure 78%
Interaction summary
HB 12
HY 2
PI 0
CLASH 5
⚠ Exposure 78%
Solvent-exposed hydrophobic surface — desolvation penalty likely
79% of hydrophobic surface is solvent-exposed (22/28 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 28
Buried (contacted) 6
Exposed 22
LogP 4.98
H-bonds 12
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.980 | Score | -29.101 |
|---|---|---|---|
| Inter norm | -0.879 | Intra norm | 0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 22 clashes; 2 protein clashes; moderate strain Δ 27.9 | ||
| Residues |
ALA24
ALA40
ALA70
ASN41
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY71
LEU39
LYS26
SER22
SER27
SER28
THR44
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 | 12 | Native recall | 0.57 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 248 | 1.69338793475606 | -0.823205 | -29.2528 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 188 | 3.395984473509757 | -0.879151 | -30.5603 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 183 | 4.97979899170821 | -0.878582 | -29.1007 | 12 | 18 | 12 | 0.57 | 0.45 | - | no | Current |
| 233 | 5.399867504176738 | -1.0007 | -35.308 | 7 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.101kcal/mol
Ligand efficiency (LE)
-0.8314kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.386
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
463.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.98
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.37kcal/mol
Minimised FF energy
97.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
706.1Ų
Total solvent-accessible surface area of free ligand
BSA total
534.1Ų
Buried surface area upon binding
BSA apolar
367.2Ų
Hydrophobic contacts buried
BSA polar
166.9Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1350.8Ų
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
548.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)