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
38.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
73% of hydrophobic surface is solvent-exposed (8/11 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 (-1.538 kcal/mol/HA)
✓ Good fit quality (FQ -13.12)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
Score
-32.303
kcal/mol
LE
-1.538
kcal/mol/HA
Fit Quality
-13.12
FQ (Leeson)
HAC
21
heavy atoms
MW
313
Da
LogP
0.51
cLogP
Interaction summary
HB 13
HY 1
PI 0
CLASH 1
⚠ Exposure 72%
Interaction summary
HB 13
HY 1
PI 0
CLASH 1
⚠ Exposure 72%
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
73% of hydrophobic surface is solvent-exposed (8/11 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 11
Buried (contacted) 3
Exposed 8
LogP 0.51
H-bonds 13
Exposed fragments:
aromatic ring (4/6 atoms exposed)aromatic ring (3/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.323 | Score | -32.303 |
|---|---|---|---|
| Inter norm | -1.654 | Intra norm | 0.115 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 13 |
| Artifact reason | geometry warning; 4 clashes; 4 protein clashes; high strain Δ 38.6 | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
ILE46
LEU31
LEU39
LYS26
SER22
SER27
SER28
THR44
| ||
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 50 | 2.701920956510862 | -1.4783 | -23.3245 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 44 | 3.0837093646972473 | -1.27765 | -22.4256 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 39 | 3.68192502547001 | -1.13113 | -16.8132 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 4.323123344014594 | -1.65365 | -32.3026 | 13 | 18 | 13 | 0.62 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.303kcal/mol
Ligand efficiency (LE)
-1.5382kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.120
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
313.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.51
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
12.23kcal/mol
Minimised FF energy
-26.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
523.5Ų
Total solvent-accessible surface area of free ligand
BSA total
486.4Ų
Buried surface area upon binding
BSA apolar
334.8Ų
Hydrophobic contacts buried
BSA polar
151.6Ų
Polar contacts buried
Fraction buried
92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1243.4Ų
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
492.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)