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 high
Native strong
SASA done
Strain ΔE
30.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.61, H-bond role recall 0.09
Reason: no major geometry red flags detected
2 protein-contact clashes
60% of hydrophobic surface is solvent-exposed (18/30 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 (-0.881 kcal/mol/HA)
✓ Good fit quality (FQ -8.81)
✓ Good H-bonds (3 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ High strain energy (30.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-29.954
kcal/mol
LE
-0.881
kcal/mol/HA
Fit Quality
-8.81
FQ (Leeson)
HAC
34
heavy atoms
MW
462
Da
LogP
2.19
cLogP
Interaction summary
HB 3
HY 7
PI 0
CLASH 2
⚠ Exposure 60%
Interaction summary
HB 3
HY 7
PI 0
CLASH 2
⚠ Exposure 60%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (18/30 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 30
Buried (contacted) 12
Exposed 18
LogP 2.19
H-bonds 3
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 2.821 | Score | -29.954 |
|---|---|---|---|
| Inter norm | -0.894 | Intra norm | 0.013 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 3 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; moderate strain Δ 30.0 | ||
| Residues |
ALA158
ALA24
ASN126
ASN41
ASP129
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU31
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 1 | Strict recall | 0.07 |
| HB same residue+role | 1 | HB role recall | 0.09 |
| HB same residue | 2 | HB residue recall | 0.18 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 148 | 2.8213603514631593 | -0.894482 | -29.9538 | 3 | 24 | 17 | 0.81 | 0.09 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.954kcal/mol
Ligand efficiency (LE)
-0.8810kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.815
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.19
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.05kcal/mol
Minimised FF energy
67.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
800.6Ų
Total solvent-accessible surface area of free ligand
BSA total
712.2Ų
Buried surface area upon binding
BSA apolar
682.6Ų
Hydrophobic contacts buried
BSA polar
29.6Ų
Polar contacts buried
Fraction buried
89.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1645.2Ų
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
493.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)