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 high
Native strong
SASA done
Strain ΔE
22.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.57, H-bond role recall 0.27
Reason: no major geometry red flags detected
1 protein-contact clashes
65% of hydrophobic surface is solvent-exposed (15/23 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 (-0.980 kcal/mol/HA)
✓ Good fit quality (FQ -9.25)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ High strain energy (22.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Internal clashes (5)
Score
-27.434
kcal/mol
LE
-0.980
kcal/mol/HA
Fit Quality
-9.25
FQ (Leeson)
HAC
28
heavy atoms
MW
386
Da
LogP
3.79
cLogP
Interaction summary
HB 9
HY 3
PI 0
CLASH 1
⚠ Exposure 65%
Interaction summary
HB 9
HY 3
PI 0
CLASH 1
⚠ Exposure 65%
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
65% of hydrophobic surface is solvent-exposed (15/23 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 23
Buried (contacted) 8
Exposed 15
LogP 3.79
H-bonds 9
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (7 atoms exposed)
| Final rank | 0.445 | Score | -27.434 |
|---|---|---|---|
| Inter norm | -1.086 | Intra norm | 0.107 |
| Top1000 | no | Excluded | no |
| Contacts | 26 | H-bonds | 9 |
| Artifact reason | geometry warning; 5 clashes; 5 protein contact clashes; moderate strain Δ 22.4 | ||
| Residues |
ALA158
ALA24
ASN126
ASP129
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU130
LEU31
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER27
SER28
THR44
THR45
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 162 | 0.4453324820837771 | -1.08645 | -27.4341 | 9 | 26 | 17 | 0.81 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.434kcal/mol
Ligand efficiency (LE)
-0.9798kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.250
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
385.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.79
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
92.45kcal/mol
Minimised FF energy
70.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
734.1Ų
Total solvent-accessible surface area of free ligand
BSA total
667.1Ų
Buried surface area upon binding
BSA apolar
622.4Ų
Hydrophobic contacts buried
BSA polar
44.7Ų
Polar contacts buried
Fraction buried
90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1560.7Ų
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
492.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)