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
20.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.38, H-bond role recall 0.27
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
58% of hydrophobic surface appears solvent-exposed (7/12 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 (-1.338 kcal/mol/HA)
✓ Good fit quality (FQ -11.62)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (61%)
✗ High strain energy (20.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-29.439
kcal/mol
LE
-1.338
kcal/mol/HA
Fit Quality
-11.62
FQ (Leeson)
HAC
22
heavy atoms
MW
324
Da
LogP
-0.18
cLogP
Interaction summary
HB 16
HY 2
PI 0
CLASH 5
⚠ Exposure 58%
Interaction summary
HB 16
HY 2
PI 0
CLASH 5
⚠ Exposure 58%
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
58% of hydrophobic surface appears solvent-exposed (7/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 5
Exposed 7
LogP -0.18
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.003 | Score | -29.439 |
|---|---|---|---|
| Inter norm | -1.399 | Intra norm | 0.061 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 16 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; moderate strain Δ 20.6 | ||
| Residues |
ALA24
ALA70
ASP68
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LYS127
LYS26
PHE38
SER22
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 | 0.38 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 314 | 0.006401770887810909 | -1.242 | -25.2095 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 3.0034143639523716 | -1.39924 | -29.4385 | 16 | 19 | 11 | 0.52 | 0.27 | - | no | Current |
| 311 | 3.4068605407179655 | -1.13086 | -24.1545 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 5.16877485116465 | -1.26971 | -25.2723 | 12 | 16 | 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
-29.439kcal/mol
Ligand efficiency (LE)
-1.3381kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.617
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
324.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.18
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-121.98kcal/mol
Minimised FF energy
-142.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
535.5Ų
Total solvent-accessible surface area of free ligand
BSA total
469.8Ų
Buried surface area upon binding
BSA apolar
286.3Ų
Hydrophobic contacts buried
BSA polar
183.5Ų
Polar contacts buried
Fraction buried
87.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1189.9Ų
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
511.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)