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
38.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.36
Reason: no major geometry red flags detected
2 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (5/9 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 (-1.754 kcal/mol/HA)
✓ Good fit quality (FQ -14.38)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
Score
-33.331
kcal/mol
LE
-1.754
kcal/mol/HA
Fit Quality
-14.38
FQ (Leeson)
HAC
19
heavy atoms
MW
287
Da
LogP
-0.05
cLogP
Interaction summary
HB 11
HY 1
PI 0
CLASH 2
⚠ Exposure 55%
Interaction summary
HB 11
HY 1
PI 0
CLASH 2
⚠ Exposure 55%
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 (5/9 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 9
Buried (contacted) 4
Exposed 5
LogP -0.05
H-bonds 11
Exposed fragments:
aromatic ring (1/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.912 | Score | -33.331 |
|---|---|---|---|
| Inter norm | -1.643 | Intra norm | -0.111 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 3 clashes; 4 protein clashes; high strain Δ 38.7 | ||
| Residues |
ALA24
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 627 | -0.6891375840801766 | -1.60782 | -29.4409 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 627 | -0.2275490505661526 | -1.42693 | -23.5246 | 9 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 0.17150852762289925 | -1.47677 | -27.9887 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 2.6118042954235654 | -1.18806 | -23.737 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 628 | 3.0283982778986456 | -1.41403 | -28.0679 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 3.911677237867414 | -1.6429 | -33.3309 | 11 | 15 | 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
-33.331kcal/mol
Ligand efficiency (LE)
-1.7543kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.379
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
287.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.05
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
9.86kcal/mol
Minimised FF energy
-28.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
489.1Ų
Total solvent-accessible surface area of free ligand
BSA total
429.1Ų
Buried surface area upon binding
BSA apolar
289.7Ų
Hydrophobic contacts buried
BSA polar
139.5Ų
Polar contacts buried
Fraction buried
87.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1222.5Ų
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
491.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)