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
34.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.68, H-bond role recall 0.45
Reason: no major geometry red flags detected
2 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (10/19 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 (-1.007 kcal/mol/HA)
✓ Good fit quality (FQ -9.51)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (34.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-28.196
kcal/mol
LE
-1.007
kcal/mol/HA
Fit Quality
-9.51
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
3.07
cLogP
Interaction summary
HB 13
HY 7
PI 0
CLASH 2
⚠ Exposure 52%
Interaction summary
HB 13
HY 7
PI 0
CLASH 2
⚠ Exposure 52%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (10/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 9
Exposed 10
LogP 3.07
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)
| Final rank | 4.828 | Score | -28.196 |
|---|---|---|---|
| Inter norm | -1.130 | Intra norm | 0.123 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 13 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; high strain Δ 34.7 | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU21
GLU73
GLY23
GLY25
LEU39
LYS127
LYS26
PHE38
SER22
SER27
SER28
THR44
| ||
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 | ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 469 | 0.6790737657746724 | -0.911602 | -25.2892 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 452 | 1.746269942367543 | -1.03441 | -26.8145 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 2.630093248716066 | -0.916314 | -25.1809 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 3.07943976914161 | -0.909128 | -22.2107 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 476 | 3.08661500064407 | -0.729748 | -18.3039 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 4.077086454438532 | -0.734575 | -17.3091 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 466 | 4.827896625512019 | -1.12997 | -28.1956 | 13 | 16 | 15 | 0.71 | 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
-28.196kcal/mol
Ligand efficiency (LE)
-1.0070kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.506
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.07
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-122.32kcal/mol
Minimised FF energy
-157.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
585.1Ų
Total solvent-accessible surface area of free ligand
BSA total
442.9Ų
Buried surface area upon binding
BSA apolar
303.7Ų
Hydrophobic contacts buried
BSA polar
139.3Ų
Polar contacts buried
Fraction buried
75.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1285.6Ų
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
527.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)