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 mixed
SASA done
Strain ΔE
20.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.39, H-bond role recall 0.36
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.428 kcal/mol/HA)
✓ Good fit quality (FQ -12.80)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (20.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-34.279
kcal/mol
LE
-1.428
kcal/mol/HA
Fit Quality
-12.80
FQ (Leeson)
HAC
24
heavy atoms
MW
326
Da
LogP
0.70
cLogP
Interaction summary
HB 16
HY 5
PI 0
CLASH 5
⚠ Exposure 56%
Interaction summary
HB 16
HY 5
PI 0
CLASH 5
⚠ Exposure 56%
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
Partial hydrophobic solvent exposure
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 7
Exposed 9
LogP 0.7
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.844 | Score | -34.279 |
|---|---|---|---|
| Inter norm | -1.476 | Intra norm | 0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 16 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; moderate strain Δ 20.4 | ||
| Residues |
ALA24
ALA40
ALA70
ASP68
GLN42
GLU73
GLY23
GLY25
GLY47
GLY71
LEU31
LEU39
LYS26
PHE38
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 597 | 0.9352703103012746 | -0.954539 | -17.403 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 608 | 2.7523442139523118 | -1.14307 | -25.1495 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 4.013237283224836 | -1.01599 | -25.8883 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 4.844010681220206 | -1.47568 | -34.2785 | 16 | 18 | 11 | 0.52 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-34.279kcal/mol
Ligand efficiency (LE)
-1.4283kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.800
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
326.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.70
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
198.15kcal/mol
Minimised FF energy
177.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
533.8Ų
Total solvent-accessible surface area of free ligand
BSA total
500.3Ų
Buried surface area upon binding
BSA apolar
356.2Ų
Hydrophobic contacts buried
BSA polar
144.1Ų
Polar contacts buried
Fraction buried
93.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1243.3Ų
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
490.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)