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
24.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.95, Jaccard 0.67, H-bond role recall 0.27
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (15/24 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 (-0.996 kcal/mol/HA)
✓ Good fit quality (FQ -9.70)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (24.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-30.875
kcal/mol
LE
-0.996
kcal/mol/HA
Fit Quality
-9.70
FQ (Leeson)
HAC
31
heavy atoms
MW
430
Da
LogP
4.70
cLogP
Interaction summary
HB 11
HY 10
PI 1
CLASH 5
⚠ Exposure 62%
Interaction summary
HB 11
HY 10
PI 1
CLASH 5
⚠ Exposure 62%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (15/24 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 24
Buried (contacted) 9
Exposed 15
LogP 4.7
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 5.444 | Score | -30.875 |
|---|---|---|---|
| Inter norm | -1.070 | Intra norm | 0.074 |
| Top1000 | no | Excluded | no |
| Contacts | 29 | H-bonds | 11 |
| Artifact reason | geometry warning; 17 clashes; 3 protein clashes; moderate strain Δ 24.1 | ||
| Residues |
ALA158
ALA24
ALA40
ALA70
ASN126
ASN41
ASP129
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 430 | 1.123128311050852 | -1.09943 | -35.0127 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 426 | 1.276767181328564 | -1.03765 | -27.4665 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 461 | 1.476372703816213 | -0.919152 | -22.5547 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 2.272725915955015 | -0.896059 | -31.1212 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 412 | 2.595705842520432 | -0.930582 | -22.1691 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 2.7191745516353594 | -0.998852 | -30.5149 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 2.7494314954702257 | -0.737507 | -24.9974 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 2.7843928705051484 | -0.713014 | -21.158 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 2.791217765151704 | -0.947142 | -35.2818 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 2.8617363901087467 | -0.750125 | -25.1003 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 2.90635541192479 | -0.798773 | -25.6886 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 2.9238440516247857 | -0.997616 | -30.3793 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 3.20302513162988 | -0.824135 | -23.5686 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 457 | 3.6279625865993608 | -1.05901 | -33.3892 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 498 | 4.00190802340201 | -0.862379 | -25.6577 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 5.080933656035169 | -0.767574 | -22.0757 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 5.444083752190545 | -1.06966 | -30.8753 | 11 | 29 | 20 | 0.95 | 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
-30.875kcal/mol
Ligand efficiency (LE)
-0.9960kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.703
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.70
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.07kcal/mol
Minimised FF energy
109.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
689.6Ų
Total solvent-accessible surface area of free ligand
BSA total
635.0Ų
Buried surface area upon binding
BSA apolar
506.8Ų
Hydrophobic contacts buried
BSA polar
128.3Ų
Polar contacts buried
Fraction buried
92.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1407.2Ų
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
497.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)